Can you continue running training whilst on antimalarials? Which ones might be best for doing so? What other points should I consider? I see if there are any answers (spoiler: there aren’t).

Training on Antimalarials

Written by Haydn Williams

At the time of writing, I am halfway through a 37-day course of Doxycycline, which does not seem to have affected my running training in any way. Increased photosensitivity is a side-effect, and I have experienced sunburn to the backs of my hands and arms whilst out for two days in the sun during Saunders mountain marathon. This was despite wearing long sleeves all day on Saturday, and all-day factor 50 suncream throughout (reapplied at at least twice each day). To safeguard against GI issues I’ve also been taking probiotics and prebiotics for the duration of the Doxy course, without any adverse effects on running training (or in general).

The daily regime.

I’ve recently been on a trip to Kenya, which meant I needed to take prophylactic antimalarials to guard against coming back with a dose of malaria. However, I was concerned as to how this might affect my running, so did a quick internet search and found… very little. There is a 2015 review from Sports Health which describes a variety of precautions to be taken when athletes are prescribed antibiotics (which is what antimalarials are). I therefore thought I’d write up what little info I did find, in case it’s of use to anyone else. This post was written in July 2019, so if you’re reading this much after that, I’d suggest a quick search of newer literature may be in order.

It’s important to note that I’m looking at prophylactic antimalarials here, i.e. those taken in advance to try and prevent the disease if you get bitten by an infected mosquito. This post does not deal with the drugs used to treat malaria if you end up with a confirmed case.

The BNF suggests that travellers to Kenya can use proguanil hydrochloride, doxycycline or mefloquine. So they were my choices:

AKA Lariam. Written off pretty quickly because there seem to be all kinds of mental health or neurological problems as side-effects. Any internet search will bring up hundreds of results, including controversy over its use by the British Army. The Journal of the Royal Society of Medicine has a summary from 2007 and there are plenty of horror stories I’ll never be able to verify.

Includes levofloxacin and ciprofloxacin. Seem to be less prevalent in the UK than the US. I discounted them almost immediately because the internet is full of stories of horrific tendon damage whilst on them, particularly the achilles. The FDA in the US states that “fluroquinolones are associated with disabling side effects involving tendons, muscles, joints, nerves and the central nervous system. These side effects can occur hours to weeks after exposure to fluoroquinolones and may potentially be permanent.“. So probably best to steer clear if you’re a runner.

AKA Malarone when combined with atovaquone. There seems to be very little out there about adverse effects of this one – it would appear to be quite safe, and I could only find one fairly useless post (in this context) which perhaps half-suggests that one person didn’t have any problems running whilst on it. Maybe. Very common side effects include sickness, dizziness, nausea and diarrhoea, though – none of which are very helpful if you’re trying to run.

The NHS has some basic information about doxycycline.

The main issue with doxycycline seems to be increased photosensitivity. Since my anti-mosquito strategy was to remain fully covered at all times, this wasn’t too much of a problem on holiday. I have had to remain careful on sunny UK days since my return, though. Doxycycline has also been reported to cause photo-onycholysis, which is the “loosening or separation of a nail from its bed”, although this seems less frequent. Potentially an issue if you’re the kind of person who loses toenails frequently whilst running (one paper I read mentioned “almost normal recovery” in the long-term, which isn’t reassuring). However, the mechanism of action isn’t known, and it’s suspected it may just be a manifestation of photosensitivity in an area which really doesn’t have much protection. So if you’re wearing shoes rather than sandals you’ll maybe be OK, I guess?

Antibiotic-associated diarrhoea (AAD) is a risk with any antibiotic, since they will wipe out your good gut flora and upset the balance of your microbiome (which is quite complex and changes over time). The Sports Health review reports an AAD rate range of 4 – 52% for Doxycycline, which is both the highest and lowest in the table, so you can come to your own conclusions about that!

One review of doxycycline safety found that 1.2% of users reported somnolence, i.e. sleepiness or drowsiness.

It has been suggested that doxycycline may have a contradictory effect to fluroquinolones when it comes to the achilles tendon – perhaps helping increase healing after surgery. I include this information only as a point of interest, rather than a sensible reason to choose doxycycline over other prophylactic antimalarials!

In light of all of the above, I chose to take Doxcycline for my trip. Any medication comes with side-effects, and it’s impossible to predict what you might or might not experience. Doxycycline had side-effects which I, as a runner, deemed acceptable. FDA data shows a rate of 13 adverse events per million doses dispensed between January 1998 and August 2003, which doesn’t seem like horrendous odds. I experienced no side effects which adversely affected my running. The only side-effect I did note was becoming sunburned incredibly easily on Saunders Mountain Marathon in Cumbria – it was a very sunny two days, but I covered up and re-applied all-day suncream several times. This would normally have been more than enough protection even for someone of my usual complexion, so I can only assume it was due to the increased photosensitivity caused by the Doxycycline.


I briefly mentioned above about the possibility of antibiotic-associated diarrhoea (AAD) with any prophylactic antibiotic. I could find little concrete evidence as to the effectiveness of probiotics in preventing this, and any reading of the literature should pay close attention to whether articles/papers are discussing using them for the prevention or treatment of diarrhoea. There is a lot of fluffy guff out there which seems to have little or no scientific basis behind it. As you’d expect, the manufacturers think that taking probiotics is a good idea for athletes, and there are articles about whether they are useful or not for athletes in general. One page I did find interesting was this one, which at least has lots of references to other sources (which I always find reassuring). The suggestion is that as well as bacteria, inclusion of the yeast Saccharomyces boulardii could be beneficial. I found plenty of products in the UK which contain both S. boulardii, along with the Lactobacillus bacteria which seem to be the mainstay of such things. It seems it’s also generally recommended that you buy a product with as many bacteria in as possible, presumably to maximise the chance of any of them making it through your stomach to actually reach the intestines. The only real side effects I could find any reference to are wind or bloat, perhaps only during the first couple of days of taking them. I couldn’t see anything suggesting they may be actively harmful. However, their effectiveness in preventing AAD remains something I’m still basically unconvinced about. I purchased them because there seemed to be no downside, but the possibility that they might keep me on the straight-and-narrow, and therefore still able to train.


Good grief, it’s like Russian dolls. Prebiotics are basically targeted food to help support the probiotic bacteria you bought after reading the section above. “Food” in this instance appears to be inulin and various types of oligosaccharides not produced by your body. I couldn’t find a huge amount of research about these, but was reassured that my inability to decide what was going on had been echoed by the authors of a Journal of Food Science and Technology paper in 2015: “Prebiotics form a group of diverse carbohydrate ingredients that are poorly understood with reference to their origin, fermentation profiles, and dosages required for health effects.“. I was unable to find any evidence that prebiotics have ever been associated with any harmful effects in general. Frankly by this point I was into the “well, it can’t do any harm!” phase so bought some anyway. I suffered no ill effects. Obviously I have no way of knowing whether they had any positive effects, but the key point in relation to the post is that they did not adversely impact upon my running training.


I’m not a doctor (well, not a medical one), so all of the above is my opinion and doesn’t constitute medical advice. You’re a grown up and you should make your own decisions about any medicines or alternative therapies you purchase, consume or otherwise partake of. I would suggest that asking a health professional is a sensible course of action.

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