Regular exercisers should expect their muscles to feel sore on the day after they exercise intensely, but if the soreness doesn't go away, they need a medical evaluation. When you exercise vigorously, your muscles are injured. Muscle biopsies taken on the day after intense exercise show bleeding into the muscle fibers and disruption of the Z-bands that hold muscle fiber filaments together as they slide by each other. The soreness you feel should usually disappear within 48 hours, and even with the most severe workouts, it should disappear within a week or two.
If the soreness remains after a few weeks, you should check with your doctor. You may have an infection anywhere in your body, an autoimmune disease or other treatable condition. Doctors may call your chronic muscle soreness fibromyalgia, chronic fatigue syndrome or multiple chemical sensitivities. These diagnoses are an admission by the physician that he hasn't the foggiest idea of the cause. There are reports of people with muscle pain and normal liver tests who are then found to have hepatitis C, which can be effectively treated. If you have urinary tract symptoms in addition to your muscle pain, you may be infected with mycoplasma or other bacteria which can be treated with antibiotics. You could have Lyme disease or some type of reactive arthritis. Don't accept a diagnosis of chronic fatigue syndrome or fibromyalgia until you have a thorough evaluation for a hidden infection or other treatable causes.