Background: Low transient transfection efficiency limits the ability to characterize putative proapoptotic gene function in neurons. Laser scanning cytometry (LSC), with its high capacity, medium throughput means of collecting fluorescent emissions from cultured cells, offers an effective technology for scoring cell death in neuronal transfectants. Methods: Cerebellar granule neurons (CGNs) were transfected with EGFP-fusion constructs of Caspase-3 and Caspase-9 using a DNA-calcium phosphate coprecipitation method. CGNs were fixed, permeablized, and stained with propidium iodide (PI) nuclear dye. An LSC method, based on a combination of Long Red Max Pixel, Long Red Integral, and Green Integral fluorescence parameters was validated for the scoring of apoptotic cell death in CGNs. Results: In Caspase-3 and Caspase-9 transfected CGNs, cell death was scored both in transfectants and nontransfected culture-mates. The cell death phenotype was found to be independent of transfection efficiency. LSC scoring of Caspase-9 transfectants was compared with visual scoring following Hoechst 33342 staining, yielding results that were similar qualitatively, but not quantitatively, likely owing to the greater sensitivity to green fluorescence of laser scanning compared to human vision. Conclusion: LSC scoring of transiently transfected CGNs offers a rapid and reliable means of characterizing proapoptotic gene effects. (c) 2006 International Society for Analytical Cytology.