It has been previously shown by morphological techniques and measurements of lysosomal enzyme levels that the I cell mutation is expressed in myoblasts but not in myotubes or mature muscle fibers. These findings suggested the possibility of developmental regulation of the affected enzyme, UDP-N-acetylglucosamine: lysosomal enzyme N-acetylglucosamine-phosphotransferase. In this article, we examine this possibility by measuring the phosphotransferase activity at various stages of muscle differentiation in three different animal species (human, chick, rat). Although activity of the enzyme is consistently higher in myoblasts than in myotubes or mature muscle, the difference in the levels of activity at these three states of muscle differentiation varies widely in the three species examined. We further found that the phosphotransferase activity was absent in the muscle of an I cell patient, in spite of normal muscle morphology. This indicates the presence of a mannose-6-phosphate-independent mechanism for lysosomal enzyme targeting in muscle and other unaffected tissues. The existence of such a pathway cannot be explained by lack of the necessary enzyme, as the phosphotransferase is present at a comparable level in normal muscle of three different species (human, chick, rat).