A capillary electrophoresis method for the direct detection of whole cell apoptosis is described. We successfully used this method to detect the apoptosis of rat cerebellar granule cells, induced by 1-methyl-4-phenyl pyridium ion (MPP+). The conditions for the detection were optimized: including the effects of running buffer pH, the voltage, and the ID of the capillaries. The effects of MPP+ concentration and apoptosis time on the relative content of the apoptotic cells were studied. The relative standard deviations of the migration time and the absorbance of the apoptotic cells were found to be 10.8 and 8.6%, respectively. The results correlated well with those obtained by using the methyl green-pironin stained experiment and DNA agarose electrophoresis.