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Why I no Longer Take Doxycycline for Malaria Prevention

doxycycline side effects
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I wrote in an earlier post of my decision not to take malaria prophylactics. This is a personal decision and I don’t necessarily recommend it for everyone. As with everything on this site, you should always consult a doctor at a travel health clinic before making such decisions. What I want to talk about today is doxycycline and the side effects I experienced when I took it for 6 months as a malaria prophylactic.

Doxy as a malaria prophylactic

Doxycycline is an antibiotic primarily used to treat a variety of bacterial infections. For example, doxy may be prescribed for Lyme disease, acne, urinary tract infections, and even pneumonia. But it’s also prescribed as a malaria prophylactic. There are three malaria prophylactics available and doxy is hands down the cheapest. In Ghana, I bought 30 capsules for a few dollars. It is taken daily, starting 2 days before your trip and continuing for 4 weeks after returning (this is because malaria can stay dormant in your liver even after you have left an area where it is endemic). If it’s the cheapest prophylactic and it does the job, what’s the problem?

My experience with doxycycline side effects

Doxycycline’s principle side effects are loss of appetite, nausea, heartburn, indigestion, and sensitivity to sunlight. There are of course a number of severe side effects that a small percentage of people may experience if they are allergic, and it must also be said that many people take doxy without experiencing any side effects at all.

Before taking it, I was concerned about the photo-sensitivity issue. I have pale skin and anything that makes me more vulnerable to the sun is potentially catastrophic. As it turns out, this side effect did not materialize for me.

What killed me was the acid reflux and heartburn. I had never experienced heartburn. No one in my family has it and I do not have a lifestyle that would make me susceptible to it (I’m not overweight, I don’t smoke, I am relatively active and I eat decently). But after taking doxy for 6 months, I now have a persistent heartburn problem that has continued for months after I quit taking it.

If you are prescribed to doxycycline, you will find a warning on the bottle that says “do not lay down within a half hour of taking this medicine.” If you don’t heed this warning, you may be in for a very unpleasant surprise. For most of my trip, I did not have any significant issues with heartburn while I was taking doxy. Nausea was the biggest side effect I felt, and I remedied this by making sure I took it with a meal.

The heartburn became an issue towards the end of my trip and it has continued even after I stopped taking doxy. I’m now taking medication to combat my heartburn (omeprazole aka prilosec)! Earlier, it caused me to postpone a trip to West Africa, because I honestly thought there was something wrong with my heart itself. The worst part was not being able to sleep. Lying horizontal continues to be a problem and if my head is not propped up, I may find myself waking up to something that feels like a combination of an asthma attack and cardiac arrest (did you know heartburn could be this awful?).

I will not be taking doxy again. If you are thinking about it as a prophylactic option, I strongly suggest discussing the possible side effects with a doctor. If you have acid reflux or heartburn in any capacity, do not even think about taking this medication.

Some other things to consider

Doxycycline is an antibiotic and in addition to taxing your liver, it actively destroys beneficial bacteria in your body. If you are planning on taking it for a while, you should look into taking probiotics to help restore your gut flora. If you eat yogurt for the same effect, you need to make sure not to eat the yogurt, or any dairy, with the dose of doxy – the medication won’t be absorbed if it’s taken with calcium.

If you have any experience taking doxycycline, please share it in the comments below.

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{ 36 comments… add one }

  • Nj September 12, 2011, 12:49 pm

    Have your GERD symptoms gone away?

    • phil September 12, 2011, 1:06 pm

      Hi Nj,
      Nope. I’m still dealing with it. I’ve been taking omeprazole and watching my diet very closely. I’m hoping I can get off the omeprazole soon, but we’ll see. I was taking 40mg a day, now down to 20 mg. Do you have GERD as well?

  • Heidi November 1, 2011, 7:38 pm

    Thank you for writing this. I have been on doxycycline and metronidazole for almost two weeks now, and I will be done on Friday. Recently I started getting bad chest pain. At first it was dull and uncomfortable and really freaked me out, but now it feels like a burning all over my chest. I mentioned it to my PCP today, and she brushed it off since she likely thinks I’m too young to have heart problems (I’m twenty-two). It really scared me, though; I took baby aspirin last night because I was afraid I was having a heart attack. If this is just a side effect caused by the antibiotic, then that makes me feel a little better. I just hope it goes away after I’m done. I’ve never experienced anything like this before! I have also lost thirteen pounds in almost a week because I have zero appetite and the thought of any food makes me feel nauseated. The side effects of these drugs are crazy!

    • phil November 1, 2011, 9:16 pm

      Yeah, it is very likely you were experiencing heartburn from the doxy. Sorry to hear this!! I have also been on doxy and metronidazole simultaneously. It’s no fun, although the metro didn’t really have too many side effects for me. Steer clear of the baby aspiring while in doxy. It will only aggravate your stomach more/produce more acid. Although, it’s totally understandable that you thought you were experiencing heart trouble. I would strongly recommend not taking doxy on an empty stomach, and also, do not lay down within 2 hours of taking it if you can avoid it!! Hope things get better for you.

  • Chris Rowson December 5, 2011, 5:46 am


    Ive been having the same problems for 4 days, I took doxy then went to bed straight after. Cant eat and its painful to even swallow water.

    Have your symptoms gone? how did you manage to get rid of it?

    Id appreciate your advice

    Warm Regards


    • phil December 5, 2011, 7:11 am

      Very sorry to hear this. If you are having short-term symptoms like this, I would get off of it and try taking something like omeprazole or even an antacid for a few days.

      My symptoms are much better now. I am taking 20mg omeprazole every other day. I stopped taking doxy a long time ago, but I had been taking it for 6 months and towards the end I started having a lot of problems. Are you taking it for malaria?

  • Amanda Tracy January 29, 2013, 3:20 pm

    I I experienced the exact same thing! I am also in great physical condition, do not smoke, drink, I exercise, and I am probably considered underweight, but I am very healthy. I was originally prescribed doxy for acne and after a couple months of taking it I had severe heartburn. I had never had heartburn before so initially I thought that I had a pill stuck in my esophagus, it was horrible. It was so bad that I too couldn’t lay down it felt like there was seriously a patch of acid burning through my chest. I was miserable, it became hard to swallow even water. Some time had passed and I was planning a trip to Thailand, not even thinking of my previous reaction, my doctor prescribed me doxycycline for malaria. After reading up on the drug I made sure to take it in the morning with plenty of food and lots to drink. I was fine until about 3 days into my trip, talk about a damper on the Thailand experience without being able to eat Thai food. It was horrible, painful, miserable, could have ruined my trip horrible, so I stopped taking it. I have been home for about 20 days and Im still battling the heartburn, its not nearly the extreme that it was, but its still irritating. I told a pharmacist about my problems and he told me to get checked for H Pykori. He also said to stay away from PPIs such as Prevacid/Prilosec as new data is showing that they can permanently effect the acid level in your stomach negatively. Zantac/Ranitidine is safer to use long term.

    • phil January 30, 2013, 8:12 am

      Hi Amanda,
      Thanks a lot for your comment. Glad to hear I am not the only one. That is not good news for me if what you say about PPIs is true. I take omeprazole (prilosec) regularly and have been doing so since summer of 2011!! I have tried to stop taking it several times, but the heartburn has always come back with a vengeance. Once I am home, I will have to visit my doc again. Do you have any links with information on these new PPI studies?

  • Maggie H August 29, 2013, 11:21 am

    Hi – My son got acid reflux a few years back and this coincided with him taking doxycycline for acne. Drugs like Prilosec are very bad for you and remove the very thing that you need to get rid of acid reflux which is stomach acid. Great book by Dr. Jonathan Wright “Why Stomach Acid Is Good For You.” Explains it very well. My son takes apple cider vinegar for it whenever he gets it now and that completely gets rid of it. A good probiotic may help too?? Lots of lemon in all drinking water. Anything to help you digest your food. A big trigger for my son is pizza – we are not sure if it is the wheat, the tomato sauce, or the dairy in the cheese – or all 3 :/ – could be the perfect acid reflux storm??

    • phil August 29, 2013, 3:17 pm

      Hi Maggie,
      I’ve tried apple cider vinegar and I do take probiotics, but neither has brought much relief. I’ve also tried aloe vera and that made a slight impact. I will try the lemon water. Thanks for the tips. I’ve come to recognize a lot of my triggers as well and that has helped. I would love to stop taking omeprazole, but I haven’t gotten there yet!

  • Maggie H August 29, 2013, 11:36 am

    Gastrazyme gets great reviews as a very helpful product too.

    • phil August 29, 2013, 3:17 pm

      ok, I will check it out!

  • maggie h August 29, 2013, 9:54 pm

    Hi Phil – It is such a bummer to have to deal with that, my son really suffered!! So glad that seems to be behind him – fingers crossed! I think that you will need to be very comprehensive in your approach. If you took omeprazole and apple cider vinegar I think they will just balance each other out and render both ineffective. So then it would appear that the apple cider vinegar wouldn’t work. My son had to take a good amount of apple cider vinegar for it to work, ie 2 tablespoons at a time. The book by Dr. Wright has a protocol that calls for Hydrochloric acid. We tried it and it seemed too strong for my son. He eats mainly Paleo now and feels that helps him also. Just some thoughts. I really hope you are able to resolve this. Good Luck. M

    • phil August 30, 2013, 4:33 am

      Hey Maggie,
      I will check out the book, it sounds like it could be very useful. Thanks a lot for your advice as well. I’m not taking a comprehensive approach right now and that’s definitely part of the problem – not being willing to make enough diet and lifestyle changes. Thanks for the inspiration, Maggie!

  • mike April 23, 2014, 3:06 am

    I am curious, you said you were on Doxy for a few months? I personally would not take any antibiotic for that long regardless of possible malaria infection. I think that is extremely dangerous; however if you had a host of ailments they are probably cured including other parasites. Doxy is pretty amazing stuff. I had to be put on Malaria meds before going to Nigeria (Cant remember the name) but you just took it while I was there and not before or after. It really did cause vivid dreams so with any medication exercise caution. I have had gerd of years now and found ranitidine the best relief not to mention it works almost immediately.

    • phil April 23, 2014, 3:49 am

      Hey Mike,
      I agree. Not a good idea to take long-term antibiotics. It sounds like you were on mefloquine also known by brand name Lariam. I took that once in 2005 and remember having insane nightmares. Per your advice, I will give ranitidine a shot. Thanks.

      • phil April 23, 2014, 3:50 am

        Ah, nevermind, this is zantac, correct? Yes, I take this. And you are right, it does provide immediate relief.

  • Susan June 26, 2014, 8:47 pm

    I’ve taken doxycycline every year for a month or more while traveling in Africa. I’m usually there for about 4-6 weeks at a time so I take Doxy for about 2 months. By the way a lot of teens take it long term for acne. Last year I started getting a sore throat while in Kenya and related it to the doxy. I stopped taking it and just really used lots of deet ..yuck. last week my doc prescribed doxy for an ear infection. I had forgotten about my reaction last year until I had taken 2 doses and my throat swelled shut so that I couldn’t swallow. I didn’t connect it to the drug though because I had some other medical issues going on. Two days later I was in the ER. I have been off the drug 3 days now and still can’t swallow. I know know it was anaphylaxis and I’m allergic to the drug. Some of you sound like you have esophagitis from taking it. Good luck. I guess I’ll take maleron now for antimalarial meds.

  • Roman C Santos October 9, 2014, 6:56 am

    I’m currently in Vietnam and taking Doxycycline as an anitmalarial. I have been on it for 4 weeks exactly now. One of the first things I noticed were headaches but those went away after a day or two. I am diabetic and soon my blood sugars started dropping but that was easily corrected with food and less medicine. Two days ago I started having severe anxiety attacks and awful acid reflux. Afraid that I was having a heart attack I googled the side effects (something I should have done BEFORE) and found this site. It seems that everything I’ve been through seems to be on the list. I am also on omeprazole for other problems but I guess I will stop that also since it seems it may also be contributing to the acid reflux. I hope this clears up soon as I still have 5 weeks before I can return to the US.

    • phil November 2, 2014, 6:40 am

      Hi Roman, if you are experiencing acid reflux that may be able to explain the heart attack sensation. I know when I first starting having symptoms, I thought that it was actually heart trouble. I wasn’t familiar with the symptoms of acid reflux, and I was honestly convinced that I was having heart palpitations or something along those lines. I would definitely visit a gastroenterologist to get a proper diagnosis, however.

  • Amanda Millard December 24, 2014, 4:47 am

    Hi, I have taken Doxy on and off for a few years with no problems. It was prescribed for my skin and I hate to admit it, but I didn’t read the leaflet that came with it. I’ve also taken more than the prescribed amount if my skin got bad! As a busy mum, I sometimes forgot to take it during the day and a few months ago I took it before going to bed, with only a tiny bit of water. I have really suffered as a result of this. The next day it felt like the tablet was stuck, but when this feeling didn’t go away and I started getting heartburn and indigestion, I started to think it was a result of taking the doxy. I’m still getting heartburn and acid reflux and I’m really worried that I’ve caused myself long term damage as I’ve read that GORD cannot be cured! I haven’t been to the doctors yet and have just been using Gaviscon. Can you offer any advice?

    • phil December 24, 2014, 5:02 am

      Hey Amanda,

      I am very sorry to hear this. I know exactly what you are going through, and I am still dealing with GERD long after I stopped taking doxy. I would definitely go see a gastroenterologist. That would be my first piece of advice. There is not any research that I can find on long term GERD caused by doxycycline, but someone should be looking into this as many people have emailed me about it now. I am on a regiment of omeprazole, and I currently take 20mg a day. I have been doing this for some time now. It is fairly effective, and I can eat and drink relatively normally without issue, although there are flair ups every now and then. Sorry I can’t be more encouraging about this. I wish I could say that it will get better over time, but that has not been the case with me.

  • Jim Matthews February 20, 2015, 11:07 pm

    I’m glad I came across this article. I’ve been on Doxy for 10 days now… I didn’t experience a problem until yesterday. I thought I had some type of food poisoning or was having a heart attack. I had no idea that indigestion could be so miserable. Thankfully today is my last day on this stuff. This article makes me feel a little better … this may not be the new norm for me! Thanks

  • suzanne edwards February 26, 2015, 7:43 am

    do you realise that taking doxy does give you thrush i had thrush in my gullet when taking this and it awfull

  • Michelle March 27, 2015, 4:59 pm

    I was prescribed doxy for acne and was taking it for a month seemingly without problem. Very similar to Amanda, busy mom, i forgot to take it with dinner. So I took it later with little water and too close to bedtime. It felt like it was stuck in my throat. The pain continued and worsened so that I felt like I had a knife in my throat and was having difficulty swallowing. I went to the ER to be told that it was most likely the doxycycline….. Why don’t they warn you of this when they prescribe it, especially for acne!!!! Anyways, I was sent to the GI specialist. Endoscopy was normal so I was sent to the ENT. Diagnosed with LPR and put on meds. Two weeks later and no relief :( and the more I research it, the more depressed I am. No one seems to recover from this. I did read of someone yesterday who found relief from Elavil. It basically calmed the nerve endings down to provide relief. She however wasn’t really having the acid issues. Still, might be worth a shot! I know I’m going to ask my doctor about it at my next visit if nothing improves….

  • Dustin April 20, 2015, 7:56 pm

    I recently went to Vietnam (almost 3 months ago) and was prescribed with doxycycline tablets. After 10 days, I experienced violent GERD symptoms and was sent to hospital. After returning home, the symptoms improved after several weeks but have never gone away completely. They are worsened with certain types of food (mostly high fat and high spice foods, and certain preservatives). It is concerning that some have reported symptoms not going away after 3 years. My doctor has prescribed nexium, however I feel terrible after taking this medicine and I am not taking it currently. I will have another visit soon, and will probably go and see a specialist.

  • Laura June 16, 2015, 7:14 pm

    Started taking this yesterday for pneumonia.. ive experienced nausea- thankfully my doctor was nice enough to prescribe me some anti sickness medication, night sweats and extreme loss of appetite. This is probably the most notable- not being one to skip meals normally, I really had to force myself to eat a boiled egg.
    9 more days to go.

  • Susie August 23, 2015, 11:16 am

    I’m so grateful to you for writing about this. I’ve been on a week’s course of Doxycycline for a sinus infection, since day 2 I’ve felt nauseous and sick, with heartburn and chest pains as you describe. I do always read information that comes with drugs and took heed of the warning about not taking it with antacid and sunlight but I didn’t notice about the water and not lying down after. It’s tiny writing on the third page – why don’t pharmas make it clear it can do this?! I also asked my GP about side effects but he said there wasn’t anything to worry about. Anyway, I really hope it doesn’t linger but at least now I know it’s not cancer of the oesophagus (the mind gets carried away when there’s no info!) thanks again x

    • phil September 24, 2015, 9:10 am

      Hey Susie,
      You know it’s really unfortunate. So many of these drugs get pushed to doctors and the side effects become less and less consequential with these efforts. I hope you are feeling better now after you stopped taking it!!!

  • Celeste November 19, 2015, 11:13 am

    I just began taking this medicine and wish I would have seen this post sooner. I have acid reflux and I just took the first does about 2 hours ago and now my acid reflux is on fire… I feel like I have a fire in my mid section and yet I am starving and scared to eat anything for a while, in fear that it will worsen the reflux…. Thanks for posting!

  • Lillian December 1, 2015, 6:34 am

    About a week ago I went to the doctor for a very bad cold that turned out to be bronchitis. I told the doctor the medications that I was currently taking, which included dexilant and zantac for acid reflux. After reading the comments about doxy, I am convinced that the doctor added fuel to the fire. Everytime that I took a doxy pill, a liquid would fill my mouth which I now know was the acid rising, I actually thought that it was the doxy that had dissolved. My acid reflux which had been getting better is now worse, I have 6 pills left which are going in the garbage. There was no warning on the instructions for doxy, but don’t you think that the doctor should have known not to prescribe doxy since I already had problems which acid reflux

  • Lakota Myers December 20, 2015, 8:10 pm

    For the second time in two months I experienced what felt like a heart attack-chest pain, nausea, tingling of extremities and weakness. I had to go to the ER in October while driving home from an out-of-state trip with my 3 kids. Frightening! My blood pressure was 189/121 and I almost passed out. After some Coumadin and testing, I was released. I have always had borderline high blood pressure and a heart murmur and sometimes a racing heart. Similar symptoms started last night. BP of 201/120! I took every home remedy I had at hand (garlic, fish oil, tumeric and magnesium) and tried to relax. After a bad night, the pattern dawned on me. Both times I had been prescribed doxycycline for a sinus infection. I will never take it again!

    • phil December 23, 2015, 12:58 pm

      Yikes. Sounds like a case similar to mine in that I didn’t notice the heartburn symptoms for what they were. Glad you found the culprit!

  • anna March 11, 2016, 10:38 pm

    I took Doxcycline 100 mg 2X/day for blepharitis for several months. Side effects were nose bleed and within one month I came down with what was diagnosed as acid reflux. I am not overweight and eat extremely healthy almost vegetarian diet. After 2 months on Kaufman’s acid reflux diet, I became worse not better. Nothing helped. Just started Protronix which has not helped – I understand it can take 6 weeks to kick in. But I started to feel, this is not a coincidence, nose bleeds and suddenly acid reflux. Then I found this post. Upper GI and barium swallow are negative, perhaps I should consider endoscopy to check further for ulcers or lacerations before I subject myself to anymore drugs that can cause future side effects.

  • ERICA March 20, 2016, 11:18 pm

    Was prescribed doxy, started taking it, noticed extreme irritability, anxiety but most of all heart palpitations. Took me a few days to realize everything, stopped the doxy but heart palpitations have continued. Anyone else have this or similar, I’ve been off doxy for 7 days, I would have thought the symptoms would have diminished by now.

  • Olivia April 5, 2016, 1:19 am

    I am relieved. I’ve been on doxy for about 5 months now due to adult acne. I’ve been fine with mild symptoms up until now. I woke up about 7 days ago in excruciating pain. It’s as everybody mentioned, I thought I was having a heart attack or heart issues. My chest was tight and tons of pressure. I went to the ER, no relief there. Then two days later, I went to urgent care – same, no answers but was given 40mg/day prescription. My chest is now filled with burning sensations and I have the inability of swallowing. Water hurts as well. It’s the most painful thing ever. I can’t imagine living the rest of my life like this. Today, the 7th day… I went to my DR to get to the bottom of this. I’m getting a H. Pylori, gotta wait three weeks on this medication, then I go back to see if I need an endoscopy. I’ve never had GERD or symptoms associated. I’m at wits ends. No answers anywhere until now. I came online to see if the doxy will affect GERD and I’ve come across your post. Ah, to my surprise. It may be the culprit. I’m just happy to finally hear possible answers. Nobody will tell me what’s wrong with me. I know, this isn’t normal. I’ve lost 10 pounds so far and everything really has me scared. I’m relieved in a sense, thank you.

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