Microcystin-leucine arginine (MC-LR), a cyclic heptapeptide produced by cyanobacteria, has strong reproductive toxicity. The present study was designed to elucidate the mechanism of declines in sperm quality as a result of exposure to MC-LR by using spermatogenic cells as a model system. MC-LR was intraperitoneally administered to male rats daily at 0, 50 and 100 µg/kg body weight for one week. Results showed that changes occurred in the structural of testis, the tubular diameter and the relative weight of the testes was significantly decreased following treatment with 100 μg/kg. Major differences in apoptosis and proliferation of testicular cells were observed at the100 μg/kg MC-LR. The gene expression levels of testis-specific histone 2B (TH2B) and transition protein 2 (TP2) were both significantly decreased. Meanwhile, the stem cell factor receptor (c-kit) was increased after exposure to 50 or 100 μg/kg MC-LR. This study demonstrated that MC-LR can alter the apoptosis, proliferation and differentiation of spermatogenic cells in vivo.