In this report, we focused on Pax3 and Pax7 expression in vitro during myoblast differentiation and in vivo during skeletal muscle regeneration. We showed that Pax3 and Pax7 were present in EDL (extensor digitorum longus) and Soleus muscle derived cells. These cells express in vitro a similar level of Pax3 mRNA, however, differ in the levels of mRNA encoding Pax7. Analysis of Pax3 and Pax7 proteins showed that Soleus and EDL satellite cells differ in the level of Pax3/7 proteins and also in the number of Pax3/7 positive cells. Moreover, Pax3/7 expression was restricted to undifferentiated cells, and both proteins were absent at further stages of myoblast differentiation, indicating that Pax3 and Pax7 are down-regulated during myoblast differentiation. However, we noted that the population of undifferentiated Pax3/7 positive cells was constantly present in both in vitro cultured satellite cells of EDL and Soleus. In contrast, there was no significant difference in Pax3 and Pax7 during in vivo differentiation accompanying regeneration of EDL and Soleus muscle. We demonstrated that Pax3 and Pax7, both in vitro and in vivo, participated in the differentiation and regeneration events of muscle and detected differences in the Pax7 expression pattern during in vitro differentiation of myoblasts isolated from fast and slow muscles.