Objectives: The experimental induction of cleft palate by Cyclophosphamide (CP) offers the possibility of detailed investigation of cleft pathogenesis. The aim of the study was to elucidate the epithelial and mesenchymal proliferation and the role of apoptosis in cleft palate specimens. Methods: Intraperitoneal application of CP at days 11 and 12 of gestation to 22 pregnant rabbits resulted in 17 bilateral clefts, 2 unilateral clefts and 15 palatal clefts in the offspring. The palatal shelves of fetal rabbit heads with clefts were compared to stages corresponding to normal palatogenesis. Immunhistochemical staining was applied to determine cell proliferation(MIB I) and apoptosis (Tunel). Results: During normal palatogenesis, a significantly higher number of apoptotic cells in the medial edge epithelium was found compared to cleft palatogenesis. Apoptosis in cleft development was observed with late fusion, under this condition the shelves in the anterior region showed signs of recovery with single apoptotic cells.The most prominent feature of cleft palate induced by CP was the reduced size of the shelves and the insufficient shelf elevation. The latter resulted in nasal epithelium on the surface of the opposing shelves. The opposing nasal epithelium was unable to fuse. Conclusion: Insufficient elevation of palatal shelves in CP induced cleft palate specimens resulted in hyperceratosis of medial edge epithelium with missing apoptosis. The depressed level of cellular activity found after treatment with CP is directly related to the reduced proliferation of mesenchymal cells and, subsequently, reduced shelf elevation and growth followed by cleft palate/ cleft lip formation.