Why are my muscles sore after I work out?

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Soreness will occur if you exercise at a higher intensity than you're accustomed to, or when you're starting a new exercise routine. The soreness that you experience is called "delayed onset muscle soreness," or DOMS. DOMS is brought on by small tears in the muscle fiber caused by stress applied on the muscle. These tears take one to two days to heal, hence the one- to two-day soreness. Once healed, the muscle is stronger than before.

(This answer provided for NATA by the Gustavus Adolphus College Athletic Training Education Program.)
Two of the main reasons why your muscles are sore after a workout is that your breaking down your muscle when you workout.  First off you create little tears in your body so they can repair and rebuild to get stronger.  The second cause is the latic acid that builds up from your workouts.  Latic acid will only last for about 24hrs.

Most of the time people will get sore following a workout that involves increased intensity, longer duration, or unfamiliar movements. Muscle soreness is a normal response to unusual movements or activities and is part of an adaptation process that leads to greater strength once the muscles recover. Small microtears and inflammation from these tears is usually what causes the soreness but is the reason that your muscles become stronger and bigger in size. Aside from the pain of muscle injuries such as strains, there are two common kinds of exercise-related muscle soreness. One has been termed acute soreness, which occurs during or immediately after your workout and the other, which usually develops 12 hours or longer after your workout, is caused by micro-trauma to the muscle tissue has been termed delayed-onset muscle soreness (DOMS). Muscle soreness during and immediately after your workout usually reflects simple muscle fatigue. If you have just begun working out, or perhaps just started an activity after a long break, you might become very sore afterwards but should keep with your new workout regiment.

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Important: This content reflects information from various individuals and organizations and may offer alternative or opposing points of view. It should not be used for medical advice, diagnosis or treatment. As always, you should consult with your healthcare provider about your specific health needs.