The p53 tumor suppressor is a transcription factor that regulates cell cycle and apoptosis in response to a variety of environmental stress conditions. Recent studies indicated that the apoptotic protease activating factor-1 (Apaf-1) is a direct transcriptional target of p53 in DNA damage-induced apoptosis. However, the dependence of Apaf-1 expression on p53 has not been shown in normal physiological conditions. To further investigate their relationship, we first examined Apaf-1 protein levels in seven organs including brain, heart, kidney, liver, lung, spleen, and testis of wild-type (p53+/+) and p53-deficent (p53-/-) mice by Western blot analysis. The heart and spleen of the p53-/- mice showed a reduced Apaf-1 protein expression compared with the p53+/+ controls, while other organs did not show significant difference. The results from Western blot analysis were further confirmed by immunohistochemistry. Semi-quantitative RT-PCR was then employed to determine the expression of Apaf-1 transcripts. Similarly, we detected a lower Apaf-1 mRNA level in the heart and spleen of p53-/- mice compared with the p53+/+ controls, supporting a transcriptional upregulation of Apaf-1 by p53. Taken together, these results demonstrate that p53 regulation of Apaf-1 expression is tissue-specific.