Chafing, Cramping, and the GI Tract: Common Running Problems and How to Solve Them

Runners are irrefutably dedicated to their training.

Unfortunately, sometimes that dedication comes at a price. Regardless of whether you’re just starting out or you’ve been training for years, you’ve likely experienced some of the extremely common bodily annoyances that come with running. Whether it be small muscle aches or a lack of bladder control, most runners have lived through it at some point. 

But, there’s good news! Because so many runners have experienced these temporary issues, there’s plenty of resources to help make them more manageable! 

So, as you’re prepping for your next run, check out the list below. You can knock out some of those annoying problems with a few of these helpful tips compiled from local runners (and non-local — thanks, internet!). 

Let’s dive into the nitty gritty!

Issues with Chafing and Bruising

Quite a few running problems are actually just a result of rubbing or chafing as you run, whether it’s on your feet or elsewhere. Thankfully, most of these issues can be easily fixed with a change in wardrobe or some easy pre- or post-run care!


Blisters are small pockets of fluid between the upper layers of the skin, often caused by friction between your skin and the material of your socks or shoes. They usually happen when your shoes are the wrong size or aren’t broken in yet, but you might also get them if your feet are sweatier than normal (think summer runs).

Common solutions include:

Chafing and Blisters

If your feet are still blistering after trying these quick tips, try switching out your socks for ones made of a different fabric. You can also try buying different protective aids like blister pads or blister prevention tape, both of which can be found in most stores with a first aid section.


Chafing is similar to blisters, but instead of creating a pocket, it causes a raw rash in areas where your skin rubs against your clothes or other skin. It tends to happen when you wear clothes that don’t fit properly (either too loose or too short). Body crevices such as the armpits and crotch are commonly affected, as are the inner thighs. 

A not-uncommon area for chafing is the nipples, particularly among men (women typically have a well-fitting sports bra to provide protection). In extreme cases, the friction of shirt fabric against skin can cause bleeding, as the skin is particularly sensitive in this area.

Common solutions include:

Chafing can be incredibly uncomfortable, and it’s often not felt until after you’re done running. A simple change of wardrobe may be just the trick to help you avoid any more irritated skin!

Black Toenails 

Black toenails can look pretty gruesome, but they’re thankfully just bruises beneath your toenails. As you run, your feet swell and, over time, your toes end up bumping against the front of your shoes, resulting in these bruises. If you frequently look like you just got your toenails painted for Halloween, it may indicate that your shoes may be the wrong size or not have a large enough toe box, resulting in too much pressure or friction on your toes.

Common solutions include:

You might feel a bit uncertain about buying shoes bigger than you’re used to, so it can be super helpful to get a professional shoe fitting! Having a professional fitting will ensure you get shoes that have enough room for your toes but still fit well enough to avoid excessive blistering and sliding.

Issues with Muscle Pains and Aching

But wait, there’s more! 

Underneath the skin lies the muscles (loosely speaking, of course), which means that once you’ve taken care of all the blistering and chafing running might throw at you, it’s time to focus on the big movers. 

The more you run, the more you’ll also probably struggle with aching muscles. Of course, these pains can happen with any workout, but they’re particularly common for runners because it can be hard to gauge what a proper rest day looks like. It’s easy to feel like you can just run through the pain, but it’s important to listen to your body!

Lucky for you, there are lots of ways to help prevent and manage these types of pains before they become a more serious injury.

Aching Legs 

Aching legs might feel like an inevitable running problem, but it’s actually super easy to lessen that mid- or post-run pain! If you experience achy legs frequently, it’s probably because your running training is either too long or too intense for your body to keep up with, and you’re not recovering enough in between runs.  

Common solutions include:

It can feel frustrating to have to lighten your load, but remember that it’s only temporary. Sometimes your body needs extra time to catch up with all your determination, but you’ll still get to where you want to be (yes, even with more gradual increases in your training)!


Cramping occurs when your muscles spasm or contract involuntarily. The condition is also commonly referred to as a Cherley Horse, particularly when the cramping occurs in the legs. Cramping can feel extremely uncomfortable or painful (especially if they last for more than a few seconds) and can quickly stop a run. Thankfully, there are multiple ways to avoid and alleviate temporary pain from cramping!

Common solutions include:

Electrolytes also play a role in muscle cramping. An imbalance of sodium, potassium, or calcum can impact your muscles’ ability to contract and relax properly. If you find yourself a frequent victim of cramping, take a look at your electrolyte consumption and try an electrolyte drink or chew or before your next run. Or, to go truly old school, run with a packet of mustard — just eat it next time your calf cramps up!

Side Stitches

Arguably one of the most common problems among runners is the side stitch. Few people can claim they’ve never felt the characteristics stabbing pain in their rib cage or abdomen after running or other intense exercise. 

The exact cause of side stitches will probably be under debate until the end of time, but explanations range from a diaphragm spasm to poor blood flow to improper breathing putting stress on the core. 

Common solutions include:

Side stitches are awful; there’s no getting around that. Sometimes, taking a short walking break and focusing on your breathing can be enough to calm your side stitch and get you back on track for the rest of your run. 

Issues with the Digestive System

Nutrition is individual and finicky even before you add running into the equation. Without having your running schedule and gastrointestinal tract in harmony with each other, there are a few annoying (and frankly somewhat embarrassing) issues that can pop up.

Not many people realize how the digestive system can react in response to running. Although many of these issues aren’t actually severe, they can be unexpected and hard to deal with for those who are newer to running.


Flatulence is extremely common—it happens a lot during any exercise, really, but especially with running and walking. Exercise speeds up your digestive process, sometimes causing discomfort in the stomach, and this essentially tells the digestive system to force a release of gas to help alleviate that discomfort.

Common solutions include:

It may be hard to completely avoid flatulence, but adjusting your fueling habits is the perfect place to start. But if all else fails, the easiest solution is to pretend like nothing happened!

Leaky Bladder

A leaky bladder, alternately called exercise-induced urinary incontinence (but who has time to say all that), is also common for many runners, but especially among females. It’s usually a result of having either weak or overactive muscles in your pelvic floor, since these are the muscles that your body uses to control urine flow (providers who specialize in pelvic floor activation can help determine which case may be causing your incontinence).

Common solutions include…

Incontinence due to running can be a touchy subject, but remember — if you find yourself affected, you’re definitely not alone. And there’s no shame in seeking treatment!

Runner’s Trots 

Runners’ trots, or runner’s diarrhea, is simultaneously one of the most uncomfortable and most common problems for runners. Research has shown that up to 60% of runners will experience the un-fun digestive malfunction. It’s usually a sign of dehydration, as there is reduced blood flow to your digestive tract as resources focus on powering your muscles. Fortunately, with the power of routine and nutrition, it’s not too hard to prevent!

Common solutions include…

If adjusting your fueling habits doesn’t seem to lessen the problem, you can talk to your doctor about alternatives, or meet with a sports nutritionist to get your diet dialed in. Runners’ trots typically aren’t severe, but there may be other factors at play that a professional can help you identify.

General Tips for Regular, Healthy Running

Ultimately, whether you’re still learning the ropes or have mastered the marathon, your body is only human! You’re likely to still experience some of the unfun problems, but it’s all part of the learning curve—you’ll learn how to go about training in due time!

While it never hurts to have a bunch of pointers for specific problems, here’s a handful of bigger-picture tips that’ll help you maintain healthy running:

There are lots of other tips you can practice, but these few are a solid start! Maintaining overall healthy running habits will not only be good for your body, but it’ll also help prevent most of these minor annoyances and potential injuries.

Hopefully you feel some relief knowing that these problems are extremely common for runners — and even more so, now that you have an arsenal of solutions! Of course, by virtue of being an internet article, the solutions here are relatively surface-level. If you have long-term issues with any of the common problems addressed here, consult with a professional, be it your running coach, physical therapist, or primary care physician. 

Keep training, keep researching—you got this!

Common Running Problems

By Megumi Kamikawa

Megumi is a graduate from San Jose State University with a degree in English, Creative Writing. Previously, she has worked as a Writing Specialist, where she served hundreds of peers in the SJSU community with her knowledge of English pedagogy. In addition to her experience with academic, creative, and professional writing, she has experience with creating visual and informational resources for various audiences. She has enjoyed taking courses on anatomy and basic physiology, and continues to educate herself in the world of health and wellness through her work with Competitive EDGE.

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