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Published levels of apoptosis in developing rat kidney (∼2.5%) seem large for a tissue with no obvious need for continual cell death. This paper examines the levels and patterns of apoptosis and mitosis in the cortical region of the developing metanephros of the mouse, the standard mammalian model embryo. Using confocal microscopy on specimens stained with propidium iodide to highlight nuclear morphology, optical sections of wholemount kidneys to a depth of ∼50 μm were analysed and mitotic, apoptotic and interphase nuclei counted in the various compartments. Of the ∼200 000 cells examined over E11.5–16.5, 2–3% were mitotic, confirming observations based on cryosections; the mitotic index peaked at E14.5, dropping to ∼0.5% by P14. The mean apoptotic index during this period was 0.28%; this figure from wholemounts was ∼10% of that earlier reported in cryosectioned rat kidneys. One possible explanation for the difference is that cryosectioning turns out to create small nuclear fragments that can stain strongly with propidium. Such fragments are not seen in wholemounts and do not stain with TUNEL. Wholemount mouse E11.5 tails and E16.5 lungs were also analysed and both their mitotic and their apoptotic indexes were similar to those in wholemount developing kidneys. These results show that the level of apoptosis in wholemount embryonic mouse kidney cortex is far less than previously reported in cryosectioned rat embryonic kidneys, and typical of that in other mouse embryonic tissues whose development seems not to require apoptosis.