Running is an exercise that benefits almost every system in your body -- it helps you lose or maintain body weight, strengthens your leg muscles and improves your cardiovascular fitness. Like any exercise worth the time, however, it entails lots of physical stresses, not only on muscles and joints but also on other organ systems, including the gastrointestinal tract. In fact, running can literally be a pain in the butt, and although running may not be the direct cause of anus pain you experience on the go, it can exacerbate existing problems.
According to Dr. Cathy Fieseler, hemorrhoids are essentially the rectal counterpart to varicose veins in the legs. Internal hemorrhoids are painless but can bleed a lot, while external hemorrhoids are tender and less prone to serious bleeding. The strain of running may cause clots to form in hemorrhoids. This is extremely painful, and the clots must be removed. Fieseler recommends staying well hydrated and coating hemorrhoids with petroleum jelly or diaper-rash cream before a run to minimize irritation. Between runs, you can use over-the-counter medications specifically for hemorrhoids.
Perhaps the most common type of anus pain runners experience is the result of chafing, which in turn is often attributable to shorts or pants not well suited to running or to clothing that becomes wet and sticky with rain, sweat or both, especially during an unusually long run such as a marathon race. Be sure not to wear anything for a long run you haven't tested a few times in shorter runs. You can apply petroleum jelly beforehand to any areas subject to chafing.
Physical problems originating in the rectum can cause pain in adjacent areas, including the anus. Mark A. Jenkins, M.D., notes that a number of conditions may be the source of this kind of pain, including age-related weakness in the muscles of the pelvic floor, rectal prolapse, irritable bowel syndrome, anal fissures, and infection. If you are unsure what's causing your pain, see a doctor for a thorough evaluation, which, if you are a woman, should include a gynecological exam.
As Dr. Jenkins says, pain in the rectum and anus may be the result of irritation of the sensory nerves serving the structures of the pelvic floor. The perineal branch of the pundendal nerve supplies nerve fibers to the anus and is commonly entrapped, impinged upon or otherwise damaged. If this happens to you, you may experience burning, increased sensitivity, a shock-like sensation, stabbing pain, twisting, or pinching while you run, and you should be evaluated by a doctor.