Gaucher disease is a lysosomal storage disorder resulting from an inborn deficiency of glucocerebrosidase. To investigate the genes responsible for the neuronal symptoms of Gaucher disease, gene expression profiles were analyzed in brains of the Gaucher disease mouse model using a cDNA microarray, and it was found that the bcl-2 gene is down-regulated. Immunoblotting and apoptosis assay were performed to study the relationship between the decreased expression of Bcl-2 and neuronal death on the brains of Gaucher mice fetuses at embryonic day 17.5 (E17.5) and E19.5. Decreased expression of Bcl-2 was observed in the brain stem and cerebellum but not in cortex by immunoblotting. In situ labeling of DNA fragmentation using terminal transferase-mediated dUTP nick-end-labeling (TUNEL) assay confirmed that apoptosis occurred in the brain stem and cerebellum. More apoptotic cells were detected in the brains of Gaucher mice fetuses at E19.5 than at E17.5. These results suggest that the accumulation of either glucocerebroside or glucosylsphingosine, as a result of glucocerebrosidase deficiency, affects gene expression and could be responsible for neuronal cell death.