Your stomach is a particularly active organ, ever secreting acids and hormones and churning up whatever is inside to prepare it for absorption downstream in the small intestine. As a result, it's a noisy organ, and it's rare to go more than a few hours without your stomach giving you an audible reminder of its presence. Running can elicit an even greater-than-normal amount of gurgling, due to the deep breathing that accompanies running.
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Chances are high that you drink a considerable amount of fluid before setting out on a run, especially a run you expect to last 45 to 60 minutes or longer. Even in mild conditions, your fluid losses can be considerable, and in hot weather you need to take in water or a sports beverage not only before the run, but also at 15-minute intervals during the run -- about 6 or 7 oz. at a time, according to exercise physiologist Pete Pfitzinger. This inevitably results in a great deal of gurgling and sloshing in your stomach. If you don't experience cramps or nausea, the noise, while distracting, is nothing to worry about.
When you run, a greater-than-usual amount of blood is pumped to your leg muscles to meet the oxygen requirements. You only have so much blood to go around, so this occurs at the expense of the blood supply to other tissues -- among them, says Dr. Gabe Mirkin, your stomach. This preferential shunting of blood from your gut to your muscles results in a marked slowing of digestion. This can cause cramps if you're not especially fit, whereas if you're well-trained, you may notice nothing more serious than a lot of gurgling noises.
Some people like to exercise a few hours after a normal meal, others like to have an energy bar or two in the hour before heading out the door, and still others swear by running on an empty stomach. If you are in the latter camp, realize that even though you may be most comfortable under these conditions, your stomach is going to remind you that it's empty, especially as your run stretches out toward an hour and your body incurs a greater calorie deficit. The idea that running on an empty stomach leads to greater fat burning is pervasive in the exercise community, but according to Jacquelyn Rudis of the USC University Hospital in Los Angeles, evidence for this idea is equivocal at best.
The act of breathing involves the creation of a negative pressure gradient between the lungs and the outside environment. At the end of a normal exhalation, these pressures are equal. The contraction of your diaphragm, a dome-like muscle attached to the bottom of your lungs, causes the diaphragm to flatten and thus move downward at its center. In doing so, it pulls the bases of the lungs with it, expanding them and causing air to rush into them to equalize the pressure. As the diaphragm moves down, it pushes against your stomach sitting just below it. Depending on the contents of your stomach, this can create some gurgling noises, with deeper breaths likely to result in more gurgling.