The soreness comes from inflammation of the muscles. If you overexercise or exercise improperly, you can make small tears in the muscle fibers. Various proteins and other material from inside the cell can then leak out. Your body's immune system sees the leaking material and tries to destroy it, creating a mild inflammation, which you feel as next-day soreness. (That's why taking anti-inflammatory drugs, like Advil, helps ease the pain.)

With training, your muscles get more resistant to exercise-induced stress and become less likely to tear or otherwise be damaged. According to Dr. Stephen Seiler, an exercise physiologist at the Institute of Sport and Health at Agder College in Kristiansand, Norway, "For the regular exerciser, next-day soreness is a sign of over-stress and definitely should not happen every day or even very often."