Sitting bone pain. Probably the most challenging sources of seat discomfort to conquer is painful "sitting bones." As shown in the diagrams, these are actually bones, called the ischium, which are part of our pelvic structure. These bones carry a the bulk of a rider's weight when sitting on a seat. Some seats are so uncomfortable that the sitting bones can start hurting within 30 minutes after the start of a ride. To get an idea of how much the sitting bones, or ischium, are involved in sitting and riding, archeologists exploring ancient Chinese grave sites supposedly can determine ages of cavalry soldiers based on how much their pelvic bones are worn.

Much of the sections on this site about modifying your seat deal with tackling this problem.

Rash. Rash is a skin irritation caused by perspiration that damages cells on the surface of the skin, and traps the sweat beneath the skin. As sweat continues to build up it causes bumps on the skin. When these bumps burst, sweat escapes into adjacent tissue, causing a stinging, uncomfortable sensation. For obvious reasons, hot, humid weather is often a culprit of butt rash. A sweaty, non-breathing riding suit or leaky rainsuit can also cause rash. Some seat pads that increase air circulation, moisture-absorbing undershorts, and breathable riding pants can all help prevent rash.

Chafing. Chafing occurs as friction against the skin causes irritation and soreness. Chafing on your buttocks while riding usually occurs when your skin presses against seams in your underwear or seat for a prolonged period. It can also happen when your thighs rub the edge of the seat that's not shaped well for the rider. A few clothing brands offer underwear (e.g., Jockey, Aerostich) that eliminates the seam on your buttocks. Some riders wear bicycle shorts to eliminate the seams, and for the extra cushion and moisture absorbtion of the padding in the crotch. If the stock seat (versus cloting) has seams that cause irritation, a new seat, seat cover, or a seat pad may be the only fix.