Regulation of epithelial cell proliferation and apoptosis are important determinants of colonic crypt homeostasis, and their dysregulations are key features of colon cancer. In this study, we investigated whether CD44, an adhesion protein overexpressed in colon cancer, plays a role in colonocyte proliferation and apoptosis, and the molecular mechanisms involved in these processes. Using a CD44 knockout mouse model devoid of a gross phenotype, we found that CD44 null colonocytes have alterations at the ultrastructural and molecular levels. Mitochondria in CD44 null colonocytes at the top of the crypt have disrupted cristae. The ratio of anti-apoptotic Bcl-xl to pro-apoptotic Bak was shifted toward apoptosis in CD44 null colon due to decreased Bcl-xl expression. Caspase 9 was upregulated and active in CD44 null colon. Its expression shifted from a location restricted to the top of the control crypts to the whole crypt axis in CD44 null colon. Caspase 3 was also activated in CD44 null colon suggesting that CD44 null colonocytes are apoptotic via the intrinsic pathway. Cell cycle regulators, cyclin A, p21, and pRb protein were abrogated in CD44 null mice. Overall, CD44 negatively regulates apoptosis via the mitochondrial pathway in the colonic epithelium through the regulators/effectors of cell cycle and apoptosis.