The implication of lysosomes in the activation of physiological cell death (PCD) was proposed some decades ago. In this work, we show that the expression of the lysosomal enzyme cathepsin D is up-regulated in developing tissues undergoing apoptosis. By comparing vital and terminal deoxynucleotidyl transferase-mediated deoxyuridinetriphosphate nick end-labeling (TUNEL) labeling patterns with in situ hybridization for this gene in a variety of tissues and organs, we show that this procedure constitutes a reliable technique to map the regions of PCD in the embryo. Using this methodological approach, we report the occurrence of two new areas of PCD in the developing limb.