To study the fate of bone cells, we used the transferase-mediated, biotin-dUTP nick end-labeling (TUNEL) assay to detect DNA fragmentation during the formation of intramembranous and endochondral bone in newly born hamsters, mice, and rats. In alveolar bone forming around the developing tooth crowns, DNA fragmentation was found in three cell types:​ TRAP-negative mononuclear cells at the bone surface, osteocytes, and some but not all nuclei of TRAP-positive osteoclasts. Osteoblasts did not undergo DNA fragmentation. A strong positive correlation was found between contacts of TUNEL-positive osteocytes and osteoclasts. Extracellular bone matrix also stained occasionally for the presence of DNA fragments. During endochondral bone formation, TUNEL staining was detected in late hypertrophic chondrocytes of the epiphyseal growth plate. During rapid longitudinal growth of long bones, TUNEL-positive hypertrophic chondrocytes were found coincident with or slightly after invasion of blood vessels from the diaphysis. However, during slow longitudinal growth and in secondary ossification centers, DNA fragmentation was seen in hypertrophic chondrocytes still located within their lacunae. We conclude that some of the osteocytes in deeper layers of bone die within their lacuna and disperse nuclear fragments over the extracellular matrix, that a majority of the osteocytes are phagocytosed and degraded by osteoclasts at sites of intense bone resorption, and that during endochondral ossification, substantial numbers of late hypertrophic chondrocyte cells undergo cell death.