Neuronal cell death is an essential feature of nervous system development and neurodegenerative diseases. Most Purkinje cells in murine cerebellar organotypic culture die when taken from 1–5‐day‐old mice (P1–P5), whereas they survive when taken before or after these ages. Using DNA gel electrophoresis, terminal deoxynucleotidyl transferase‐mediated dUTP nick‐end labelling (TUNEL) and electron microscopic analyses, we were able to show that this massive Purkinje cell death is apoptotic in nature and reaches a peak at P3. From the several endogenous genes known to be involved in the apoptotic process, we have focused on two: the bcl‐2 and the caspase‐3 that encode for anti‐apoptotic and pro‐apoptotic proteins, respectively. Immunostaining for activated Caspase‐3 correlated with Purkinje cell death. A better survival of Purkinje cells was observed in P3 slices taken from hu‐bcl‐2 transgenic mice, and in slices treated with z‐DEVD.fmk (an inhibitor of numerous caspases). Thus, these two genes are implicated in the age‐related Purkinje cell apoptosis in organotypic culture. As Purkinje cell death in vitro takes place at the same age as Purkinje cells engaged in intense synaptogenesis and dendritic remodeling in vivo, we propose that this apoptosis reflects a naturally occurring Purkinje cell death during this critical period.