Nucleosomal DNA fragmentation is detected in myoblasts only when apoptosis is induced under differentiating conditions. However, the molecular mechanisms and the DNase responsible for the differentiation-dependent apoptotic DNA laddering are poorly understood. Here we show that a Ca 2؉ /Mg 2؉ -dependent endonuclease, DNase ␥, is induced in C2C12 myoblasts during myogenic differentiation and catalyzes apoptotic DNA fragmentation in differentiating myoblasts. A Ca 2؉ /Mg 2؉ -dependent, Zn 2؉ -sensitive endonuclease activity appears in C2C12 myoblasts during myogenic differentiation. The enzymatic properties of the inducible DNase were found to be quite similar to those of DNase I family of DNases. Reverse transcriptase-PCR analysis revealed that the induction of DNase ␥, a member of the DNase I family of DNases, is correlated with the appearance of inducible DNase activity. The induction of DNase ␥ occurs simultaneously with myogenin induction but precedes the up-regulation of p21. A high level of DNase ␥ expression was also detected in differentiated myotubes but not in skeletal muscle fibers in which DNase X is highly expressed. The role of DNase ␥ in myoblast apoptosis was evaluated in the following experiments. Proliferating myoblasts acquire DNA ladder producing ability by the ectopic expression of DNase ␥, but not DNase X, suggesting that the expression level of DNase ␥ is the determinant of the differentiation-dependent apoptotic DNA laddering observed in myoblasts. DNA fragmentation during differentiation-induced apoptosis is strongly suppressed by the antisensemediated down-regulation of DNase ␥. Importantly, the extent of DNA laddering is well correlated with the level of endogenous DNase ␥ activity. Our data demonstrate that DNase ␥ is the endonuclease responsible for DNA fragmentation in apoptosis associated with myogenic differentiation.