Objective To investigate the role of ceramide regulation on the alcohol-induced neuronal cells apoptosis in mice. Methods Using sphingomyelin synthase 2 knockout (SMS-/-2) mice and wide-type (WT) mice to establish the model of prenatal alcohol exposure. A total of 360 pups from control the group and ethyl alcohol (EtoH) treatment group was used in the study. The levels of serum sphingomyelin (SM) was detected with enzymatic method in P0. Apoptosis of mossy cells in hippocampus were investigated after alcohol exposure with immunofluorescent labeling. The expression of activated Caspase-8 and activated Caspase-3 in hippocampus were tested with Western blotting analysis. Results In WT and SMS-/-2mice, prenatal alcohol exposure down-regulated the SM levels with dose-dependency ( EM>F /EM>=41.08,EM> P/EM> <0.05). The SM level of serum in SMS-/-2 pups was significantly lower than that of WT pups( EM>F/EM> =53.34, EM>P/EM> <0.01). In both WT and SMS-/-2pups, the number of apoptosis moss cells in hippocampus was increased after prenatal alcohol exposure with dose dependency ( F =15.61, P <0.05), and then decreased with the growing age. However, compared with the WT pups, the number of apoptosis neurons in hippocampus of SMS-/-2 pups increased more than WT mice ( EM>F /EM>=11.72, EM>P /EM><0.05). Western blotting supported the results of immunofluorescent labeling. Conclusion The reduction of SM level in SMS-/-2 mice leads to the ceramide accumulation in brain tissue. Ceramide is involved in prenatal alcohol exposed neuronal apoptosis in the process, and may promote apoptosis. Alcohol exposure during pregnancy, mainly through the death receptor pathway, induces neuronal apoptosis.