Busulfan is a widely used cancer chemotherapeutic agent. Temporary or permanent sterility in male patients is one of the most common side effects of this drug. The present study was performed to evaluate the changes in the microscopic structure of the testes of prepubertal rats, as well as the changes in PCNA and caspase-3 immune expression, at different durations after busulfan administration. The rats were 5 weeks old and were divided into two main groups. Control group and busulfan treated group. Busulfan treated group received a single dose of busulfan (40 mg/kg), then animals were subdivided to three subgroups; IIa, IIb, IIc which were sacrificed after four, ten and twenty weeks, respectively, from the beginning of the experiment. Light and electron microscopic studies were done. Serum testosterone level and relative testes weight were assessed. Immunohistochemical staining for anti-proliferating cell nuclear antigen (PCNA) and anti-caspase-3 antigen was also done. Morphometric and statistical studies were carried out. Group II revealed histological and ultrastructural degenerative changes including congested blood vessels and degenerated spermatogenic epithelium, Sertoli cells, and Leydig cells. These changes were more evident after 10 weeks of busulfan administration and were accompanied by absence of mature sperms in the lumen of seminiferous tubules. These changes were associated with a significant reduction in relative testes weight, testosterone level, germinal epithelial height and seminiferous tubule diameter. Moreover, PCNA and caspase-3 immune expression was significantly altered in busulfan treated group. Mild improvement in testicular structure was observed 20 weeks after busulfan treatment. [ABSTRACT FROM AUTHOR]