What causes the Pain in your side you may occasionally feel while Running

Work those abs. Stronger abdominal muscles will do a better job of limiting the jarring on your internal organs and thus limiting the strain on the ligaments connected to the diaphragm.
Avoid taking shallow, quick breaths. Breathe deeply and methodically while you are doing a jarring exercise.
As noted, most people exhale as they land on one foot or the other. It turns out, about 70% of people exhale when they land on their left foot rather than their right. This is a good thing and will help prevent side stitches. When you exhale when landing on your right foot, it particularly causes extra strain on the ligaments between the liver and diaphragm, as well as added friction between the two. This is why most side stitches occur on the right side rather than the left. Thus, if you are in a race and you can’t stop just because of a side stitch, focus on exhaling when your left foot lands, instead of your right, as well as taking deep methodical breaths, rather than short quick ones as noted above. If, in this “can’t stop” case, you have a very rare left side stitch, focus on exhaling when your right foot strikes the ground until the side stitch goes away.
Stretching will also help reduce the likelihood and help get rid of side stitches. Before running or doing some other jarring activity, warm up then do various abdominal stretches. If you already have a side stitch, try doing this simple stretching exercise while walking. Reach towards the sky as you inhale and let your arms slowly fall as you exhale. This will help relieve some of the tension in your diaphragm and help get rid of the side stitch.
An alternative to the “reach for the sky” method is to press your fingers deeply into the area the pain is coming from and massage the area firmly while deeply breathing. This should accelerate the demise of the side stitch.
Another preventative method is to avoid eating much of anything two or three hours before doing the jarring activity. An empty stomach takes up less room in your abdomen and is also lighter. Both of these things will help reduce the strain on the ligaments between the diaphragm and the stomach. As an added bonus, an empty stomach will also help you burn fat faster. Once your body runs dry of its readily available fuel stored in your muscles (glucose) and then liver (glycogen), it will look to your stomach for some makings of glucose (simple and complex carbohydrates). If the stomach is empty or otherwise lacks what your body needs there, it will switch gears and start getting what it needs from your body’s stored fat. Whether getting what it needs to make glucose from the contents of your stomach or from fat, you’ll feel this kick in when you get your “second wind”.

Bonus Facts:

Appendicitis can sometimes feel a bit like a side stitch, in the early stages. If you find you have a “side stitch” that sticks around for more than a few minutes after a side stitch normally should have gone away, you may want to go get that checked out to make sure you aren’t having appendix problems.
If your side stitch spreads all the way up to your shoulder, you may not have a typical side stitch at all; you may be having a “mild” heart attack.
About 70% of regular runners report experiencing side stitch at least once a year.
For those who don’t know, a “thoracic diaphragm” or more typically just “diaphragm” is an internal muscle that extends across the bottom of your rib cage. It has a few functions; one of which is it separates your lungs, heart, and ribs from your abdominal cavity. In humans, the diaphragm is also extremely important in breathing, as well as important in aiding in defecating, urinating, and vomiting; all of these by increasing abdominal pressure. It also helps in preventing acid reflux by exerting pressure on the esophagus.

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