Decreased estrogen production is associated with changes in the skeletal, cardiovascular and muscular systems. At the level of skeletal muscles, it has been shown that a reduction in force production occurs at menopause but the underlying mechanisms are still unknown. The aim of the study was to investigate the effects of ovariectomy on myosin heavy chain (MyHC) composition. Additionally, we studied the effects of physical activity and the combined effects of physical activity and estrogen treatment on MyHC content in ovariectomised (OX) animals. Twenty-five rats were randomly assigned to five different groups: controls, runners, OX, ovariectomised runners and ovariectomised runners receiving estrogen. Exercise consisted of voluntary running for 5 weeks. Two muscles were analysed: m. extensor digitorum longus, EDL, (fast muscle) and m. soleus (slow muscle). MyHC content was analysed on 8% gel electrophoresis. The level of running activity is reduced in OX animals and estrogen administration is associated with the normalisation of the level of physical activity. Ovariectomy induces a shift from fast to slow MyHC isoforms in both the soleus and EDL. When OX animals are allowed to run, alterations in MyHC isoforms are still observed in the EDL but not in the soleus. When physical activity is combined with estrogen treatment no alterations are observed in both muscles. In conclusion, this study shows that ovariectomy induces alterations in the contractile properties of skeletal muscles and that physical activity in combination with estrogen treatment are associated with the maintenance of slow and fast muscle characteristics.