You’re two miles into what should be your best run this week when that familiar cramping starts.

Your pace slows, your form suffers, and suddenly you’re scanning the horizon for the nearest porta potty or somewhere you can duck on the side of the trail where no one will see you.

Sound familiar?

If you’re like most runners I know, this is an all-too-familiar scenario.

But, why does this keep happening? Is it something you ate? Poor timing? Bad genetics?

Well, that’s what we’re going to dive deep into in this article. You’ll learn:

• The science of what actually happens in your gut when you start running (without all the medical jargon)
• Show you the research on the two main mechanisms that trigger bathroom emergencies during runs
• Explain why some runners seem immune to these issues (spoiler: they’re not, they’ve just adapted differently)
• Give you the specific, evidence-based strategies that research shows can prevent these problems before they start

So, if you never start a run without toilet paper tucked into your shorts or you know where every porta potty is on all your running routes, then this is a must-read.

First, You’re Not the Only One

If it helps you feel better about the situation, you’re definitely not alone in dealing with this issue.

Research shows a staggering 30-90% of endurance athletes experience gastrointestinal symptoms during training and competition [1].

In fact, a landmark study of 471 marathon runners found that 83% of respondents indicated they occasionally or frequently suffered one or more GI disturbances during or immediately after running [2].

The most common symptoms break down into two categories:

Upper GI symptoms include nausea, heartburn, bloating, and stomach cramps. These tend to be more common in women than men and more prevalent in younger runners compared to older athletes.

Lower GI symptoms are what most runners fear most: the urge to have a bowel movement (53% of runners) and diarrhea (38% of runners). These symptoms are especially common among female runners, affecting 74% and 68% respectively [2].

The research is clear on this: exercise-induced GI distress is a widespread issue and is a major fear runners have, both in training and when racing.

That’s why understanding the mechanisms behind these symptoms is so critical for improving both your health and running performance.

The Blood Flow Issue

When you lace up your running shoes and head out the door, your body immediately begins a complex process of resource allocation, i.e. concentrating its efforts on the processes that are most important in the moment.

Unfortunately for your digestive system, it’s not the priority.

The digestive system needs blood flow to function efficiently, but as soon as you start running your body diverts blood rom your digestive system to fuel your working muscles, heart, and lungs.

In fact, research has shown that blood flow decreases by 20% within just 10 minutes of running, and by a dramatic 80% after 1 hour of running at 70% of your VO2max [3].

This isn’t necessarily a bad thing in the short term, it’s how your cardiovascular system prioritizes survival during physical exertion.

But it does create problems for your gut.

Without this blood flow, your gut doesn’t have the oxygen and nutrients it needs to supply the digestive organs, transport absorbed nutrients from the gut to the rest of the body, and remove waste products.

This reduced efficiency impairs digestion and actually accelerates the movement of food through the intestines. This, combined with the physical jostling of running, is what leads to cramping, diarrhea, and a sudden urge to use the bathroom.

The Heat Stress Double-Whammy

Unfortunately, the normal blood flow issues involved with running are only part of the problem.

The second major mechanism involves heat stress, and this is where things get really interesting from a scientific perspective.

First, as your body heats up, both from the running you’re doing and any outside factors, such as the temperature and humidity, blood is further diverted away from the digestive system and allocated to cooling itself.

So, both increased duration (the longer you run, the more warm your body will naturally get) and increased temperatures create a compounding effect on your digestive system.

Moreover, recent research has identified that when your core temperature reaches 38.5°C (101°F), intestinal permeability increases [4].

This often called “leaky gut” or, more scientifically, “exercise-induced gastrointestinal syndrome”, and is estimated to affect 70% of endurance athletes [6].

The “Leaky Gut” Connection

You may have heard the term “leaky gut” thrown around before, but never really knew what it meant.

Well, basically what happens is that stress in the gut (from heat, lack of blood flow, and jostling) causes intestinal damage and increases intestinal permeability.

In layman’s terms, this is like developing tiny holes in your gut lining that allow things to pass through that normally shouldn’t. This includes bacterial lipopolysaccharides, also known as endotoxins.

When these endotoxins leak into your bloodstream, they trigger an acute-phase inflammatory response, including the release of interleukin-6 in response to an increasingly endotoxic environment [5].

This inflammatory response is part of what causes the cramping, nausea, and urgent bathroom needs you experience during runs.

The Question Remains: What Can We Do About It?

So, now that we have a better understanding of what’s going on we can begin to formulate some specific strategies for how to combat this.

Luckily, in recent years there’s been some groundbreaking research on the strategies that can significantly impact exercise-induced GI distress.

Support digestion with targeted probiotics

The first evidence-based strategy is to create a more favorable environment in the gut with probiotics.

Probiotics almost seem to be a buzzword these days with many influencers claiming that they are the treatment for nearly every ailment we have. And while I do think they are a bit overhyped in some instances, they do have a little of scientific evidence to support their efficacy when it comes to digestion.

Probiotics are a combination of live beneficial bacteria and/or yeasts that naturally live in your body and that can be used to change or re-establish the intestinal flora and improve your health.

Probiotics have some pretty well-supported research showing they can…

• Break down food and extract nutrients, making it easier for the body to absorb.
• Improve the integrity of the gut lining, which helps prevent the leakage of undigested food particles (the leaky gut mentioned earlier) and enhances nutrient absorption.
• Reduce gut inflammation to increase the absorption of micronutrients like calcium and iron.

But, not all probiotics are created equal.

Probiotics come in many different strains and formulations, all of which help target specific aspects of the digestive system and can help in different ways.

In the case of runners dealing with stomach issues, two strains stand out above all: Bifidobacteria and ProbioSEB Duo.

Bifidobacteria

This strain is important because they help digest fiber and other complex carbs that you need to fuel your training properly, yet can be difficult for your body to digest on its own, which can lead to bathroom issues.

Specifically, bifidobacteria supplementation has been shown in research to significantly lower the incidence and severity of GI symptoms in marathon runners [10].

Research has also shown that runners who supplemented with bifidobacteria saw a reduction in the severity of GI symptoms during training as well as a reduction in the duration of GI symptoms post-race [11], [12].

There is also some evidence that the bifidobacteria strain can improve carbohydrate absorption and metabolism during endurance exercise, potentially sparing muscle glycogen during prolonged activity.

ProbioSEB Duo

The probiotic bacteria in ProbioSEB Duo help create a favorable environment for the growth of “good microflora” in the large intestine.

This good mircroflora can make your digestive system more efficient (so it’s impacted less when blood flow is reduced) and helps absorption of water and nutrients and passage of waste products.

More importantly, unlike most probiotics that get destroyed in hot conditions (like when we run), ProbioSEB Duo withstands extreme conditions to successfully reach its destination within the body at full power.

It’s one of the few probiotics that can actually be utilized during running.

Start your runs with an empty gut

Since we know the main cause of stomach and bathroom issues while running is a slow down of the digestive system, starting your runs with an empty gut will help eliminate many of the problems this causes.

Since you’re reading this, I can probably assume you’ve tried changing your pre-run and even your night-before nutrition to eat foods that will be digested quickly and are easy on the stomach.

This is definitely a good step, but as you’ve likely noticed, it doesn’t always work.

Luckily, there is one relatively new ingredient we’ve seen make a huge difference: Psyllium seed husks.

Psyllium seed husks are the outer covering of the Plantago ovata plant’s seeds and are a source of soluble fiber and have been shown in research to help make bowel movements easier and more consistent.

Compared to similar fibers, psyllium is less fermentable in the gut, which means it’s less likely to produce flatulence, stomach pain, and nausea [14].

Taking psyllium in the evening helps ensure you can evacuate completely before your morning run.

Psyllium seed husks can also help add bulk to stool, which helps relieve the feeling of needing to go to the bathroom. This is especially helpful due to the jostling that occurs in the digestive tract during running.

Heat stress protection

The final element we need to address is dealing with the exertional stress excess heat causes to the gut.

And, once again, some ground-breaking new research seems to have found a solution to this problem.

New Zealand blackcurrant extract, rich in anthocyanins, has been shown in research to effectively protect and strengthen the gut lining, mitigating heat stress and improving thermoregulation.

In one study, participants who supplemented with New Zealand blackcurrant for 7 days and then raced in hot conditions experienced a 40% reduction in heat-induced cell damage and “leaky gut”.

In a separate study, blackcurrant was shown to reduce total gastric distress symptoms in runners by 73%.

There is also some newer research, unrelated to gut health, that shows blackcurrant may be an overall performance-enhancing supplement as well.

• Increase the body’s reliance on fat for energy during exercise, which could also contribute to better performance [15].
• Improvement of 38 seconds in 5k performance compared to placebo [16]
• Average improvements of 38 seconds, compared to placebo

More research is definitely needed in these cases, but there’s no doubt that blackcurrant extract may be a game-changer for runners battling heat-induced GI issues.

With its ability to provide quick relief and enhance performance, it may be worth considering adding this supplement to your pre-race routine

Putting it All Together

While almost any probiotic or gut health supplement will help improve your overall digestive health, you have unique challenges and needs as a runner that generic probiotics just don’t address.

If you suffer frequently from stomach and bathroom issues while training and racing, or you just want to improve your overall gut health, I highly recommend checking out MAS Flush.

Their probiotic is specifically designed to address the exact needs and stomach issues endurance athletes face when training and racing hard.

To my knowledge, it’s the only probiotic targeted specifically to endurance athletes that also addresses the common issue of runner’s trots and needing to go to the bathroom when running.

Here’s the link to check out their product: https://masedge.com/flush-for-runners/

As a note, MAS Edge is a long-time partner of Runner’s Connect. We partnered with them specifically because all of the products are designed specifically for endurance athletes and because they are on the cutting-edge when it comes to the latest research.

The Bottom Line: Your Gut Doesn’t Have to Sabotage Your Running

The research on exercise-induced gastrointestinal distress has evolved significantly in recent years, giving us clear insights into the mechanisms behind these frustrating symptoms.

We now understand that GI issues during running are caused by two specific, measurable physiological processes: reduced splanchnic blood flow and heat-induced intestinal permeability. The combination creates a perfect storm for digestive distress that affects the vast majority of endurance athletes.

Luckily, recent years have brought groundbreaking research showing that evidence-based interventions targeting these specific mechanisms can provide significant relief. The key is finding what works for your individual situation and remaining consistent with the approaches that show the most promise in the scientific literature.

For the time-constrained runner, this means implementing strategic carbohydrate timing, considering targeted supplementation that addresses exercise-specific digestive challenges, and being mindful of environmental factors that amplify these issues.

The practical takeaway is that you don’t have to accept frequent bathroom emergencies as an inevitable part of your running experience. With the right evidence-based approach, you can significantly minimize these issues and focus on what really matters: enjoying your runs and achieving your performance goals.