A muscle progenitor cell population, other than muscle satellite cells, can be isolated and purified from porcine muscle tissue. We show the presence of at least two types of stem cells in porcine muscle: those that express α6 integrin and those that lack expression of this integrin type. By flow cytometry, we could select for myogenic stem cell populations expressing the neural cell adhesion molecule in the presence and absence of α6 integrin. The expression of α6 integrin showed an advantage in the formation of myotubes, possibly by an improved cell fusion capacity. This notion was strengthened by qRT-PCR analysis showing sustained PAX7, MYF5 and DESMIN expression and a strong myogenic differentiation capacity of this stem cell population. Selective inhibition of α6 integrin function, both by blocking antibodies and RNA interference, showed the importance of α6 integrin in myogenic differentiation of muscle stem cells. It is concluded that α6 integrin expression can be used as biomarker to select for highly myogenic cell populations in muscle tissue.