The aim of this study was to characterize the activation of caspase-3 along the crypt/villus axis in the normal and irradiated intestine and to compare active caspase-3 expression with existing apoptosis detection techniques. Small and large intestine were removed from mice at various time points after exposure to 8 Gy γ-radiation. Positive apoptotic cells stained with an antibody against active caspase-3, haematoxylin and eosin (H&E) or TUNEL were scored in histological sections of small and large intestinal crypts and villi. In the control intestine, active caspase-3 expression was rarely observed; however, expression was markedly increased following exposure to radiation and was predominantly confined to apoptotic bodies. Measurement of apoptosis in intestinal crypts using active caspase-3 expression gave similar results to apoptosis detected from H&E-stained sections. In the normal villus, active caspase-3 expression was observed infrequently and did not significantly increase following radiation, consistent with a lack of apoptotic body formation from H&E sections. This study indicates that caspase-3 is activated in intestinal crypts but not in villi following γ-radiation. Active caspase-3 detection compared favourably with existing immunological techniques, suggesting that it is a suitable alternative method for apoptosis quantification. Copyright © 2001 John Wiley & Sons, Ltd.