Nearly 90% of endurance athletes experience gastrointestinal distress during competition, yet most runners spend countless hours training their legs while completely ignoring their gut.
If you’re targeting your next half marathon, marathon, or ultra-distance event, your digestive system needs just as much preparation as your cardiovascular system.
The difference between a personal best and a portable toilet pit stop often comes down to how well you’ve trained your gut to handle fuel at race pace intensity.
In this comprehensive guide, you’ll discover…
- The physiological reasons why your stomach rebels during hard efforts
- Learn progressive protocols to train your digestive system like any other body system
- 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.
The Hidden System: Why Your Gut Matters as Much as Your VO2 Max
Your digestive system represents the often-overlooked fourth pillar of endurance performance, alongside cardiovascular fitness, muscular strength, and mental toughness.
Research from Dr. Trent Stellingwerff [1] demonstrates that gastrointestinal problems are the primary cause of DNFs (did not finish) in ultra-endurance events, surpassing even musculoskeletal injuries.
The physiological demands of processing 200-400 calories per hour while maintaining race pace create a perfect storm of digestive challenges.
Simply put, your gut needs training just like your heart and muscles.
Understanding Exercise-Induced GI Distress
The Blood Flow Diversion Effect
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.
The Mechanical Trauma Factor
The repetitive jarring motion of running creates additional stress on your digestive system.
Each foot strike sends shock waves through your abdominal cavity, causing what exercise physiologists term “mechanical trauma” to your internal organs.
Studies show [3] that this repeated impact can damage the intestinal lining, leading to increased permeability – commonly known as “leaky gut syndrome” in endurance athletes.
The combination of reduced blood flow and mechanical stress creates the perfect environment for nausea, cramping, and urgent bathroom needs.
The Absorption Bottleneck
Your small intestine can only absorb a limited amount of carbohydrate per hour, regardless of how much you consume.
Research consistently demonstrates [4] that the maximum absorption rate for glucose is approximately 60 grams per hour, while glucose-fructose combinations can increase this to 90 grams per hour.
Consuming more than your gut can absorb leads to osmotic overload – excess carbohydrates sitting in your intestinal tract, drawing water from your bloodstream and causing bloating, cramping, and diarrhea.
This physiological ceiling explains why more fuel doesn’t always equal better performance.
Progressive Gut Training: Your Systematic Protocol for Digestive Adaptation
Phase 1: Foundation Building (Weeks 1-4)
Start with tolerance training during your easy runs when blood flow to the gut is less compromised.
Begin consuming 30-40 grams of carbohydrates per hour during runs lasting 90 minutes or longer.
Use your planned race-day products during these sessions to begin the adaptation process.
A study by Stellingwerff and Cox [5] found that regular carbohydrate consumption during training significantly improved gastrointestinal tolerance during subsequent testing.
Focus on single-source carbohydrate products (glucose or maltodextrin) before progressing to more complex formulations.
Phase 2: Volume Progression (Weeks 5-8)
Gradually increase your hourly carbohydrate intake to 50-60 grams per hour during longer training sessions.
Introduce dual-source carbohydrates (glucose + fructose) to train the SGLT1 and GLUT5 transporters in your intestinal lining.
Research from Jeukendrup and colleagues [6] demonstrates that these transporters can be upregulated through consistent training, increasing your absorption capacity.
Practice fueling every 15-20 minutes to establish a feeding rhythm that becomes automatic on race day.
Phase 3: Intensity Integration (Weeks 9-12)
Begin incorporating fueling during tempo runs and marathon-pace efforts when gastrointestinal blood flow is more restricted.
Target 60-70 grams of carbohydrates per hour during these higher-intensity sessions.
This phase teaches your digestive system to function under the stress conditions you’ll face during competition.
Studies show [7] that athletes who practice fueling at race intensity experience significantly fewer GI issues during actual events.
Phase 4: Race Simulation (Weeks 13-16)
Execute full dress rehearsals during your longest training runs, consuming 70-90 grams of carbohydrates per hour for runs lasting 2.5 hours or more.
Practice your complete race-day nutrition strategy, including pre-race meal timing, during-exercise fueling, and hydration protocols.
This final phase ensures your digestive system is fully prepared for the demands of race day.
Product Testing: The Systematic Approach to Finding Your Formula
The Elimination Protocol
Start with the simplest possible fueling strategy and systematically add complexity.
Begin with single-ingredient products like pure glucose or maltodextrin during your foundation phase.
Research indicates [8] that simpler carbohydrate sources are generally better tolerated during exercise than complex formulations.
Document your response to each product using objective metrics: energy levels, GI comfort, and performance markers.
The A/B Testing Framework
Test only one variable at a time to isolate what works and what doesn’t.
If you’re comparing gels versus sports drinks, keep all other factors constant: timing, quantity, and additional nutrition.
A systematic review by Burke et al. [9] emphasizes the importance of individualized nutrition strategies based on personal tolerance testing.
Create a detailed log documenting product type, quantity consumed, timing of consumption, exercise intensity, and any GI symptoms experienced.
The Concentration Testing Method
Test different concentrations of the same product to find your optimal osmolarity.
Many athletes assume that more concentrated solutions provide better energy delivery, but research shows [10] that highly concentrated carbohydrate solutions can actually impair gastric emptying.
Start with 6-8% carbohydrate solutions and adjust based on tolerance and absorption rates.
Monitor how different concentrations affect your perceived exertion, energy maintenance, and GI comfort during training sessions.
The Environmental Stress Test
Practice your nutrition strategy under various environmental conditions that mirror your goal races.
Hot weather significantly impacts gastric emptying and fluid absorption, while cold conditions can affect your desire to consume fluids and gels.
Studies demonstrate [11] that heat stress can reduce gastric emptying by up to 50%, dramatically affecting your fueling strategy effectiveness.
Test your protocols during hot training sessions, early morning runs, and varying humidity conditions to ensure consistent performance across race day scenarios.
Fine-Tuning Your Digestive Performance
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 some 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.
Implementation Timeline: Your 16-Week Gut Training Schedule
Weeks 1-4: Establish Baseline Tolerance
- Consume 30-40g carbohydrates/hour during easy runs >90 minutes
- Use single-source carbohydrate products only
- Document all responses in detailed training log
- Focus on establishing consistent fueling intervals
Weeks 5-8: Progressive Volume Loading
- Increase to 50-60g carbohydrates/hour during long runs
- Introduce glucose-fructose combinations
- Practice fueling every 15-20 minutes
- Begin environmental condition testing
Weeks 9-12: Intensity Integration Phase
- Fuel during tempo runs and marathon-pace sessions
- Target 60-70g carbohydrates/hour at higher intensities
- Test complete hydration and fueling protocols
- Refine product preferences based on tolerance data
Weeks 13-16: Race Simulation Mastery
- Execute full race-day nutrition during longest runs
- Consume 70-90g carbohydrates/hour for 2.5+ hour sessions
- Practice pre-race meal timing and composition
- Finalize backup fueling strategies for race contingencies
The Bottom Line: Your Gut is Trainable
Your digestive system responds to progressive training just like your cardiovascular and muscular systems.
The research is clear: athletes who systematically train their gut tolerance experience significantly fewer race-day GI issues and maintain higher carbohydrate absorption rates during competition.
Start your gut training protocol immediately, regardless of where you are in your current training cycle.
Even four weeks of consistent practice can dramatically improve your digestive performance during endurance events.
Your next personal best might depend less on your VO2 max and more on how well you’ve taught your stomach to fuel your ambitions.
