Polycystic Ovary Syndrome (PCOS) is a common endocrine-reproductive disease in females. PCOS patients show decreased ovary granular cells, which is possibly related with cell apoptosis. This study thus aimed to investigate the apoptotic mechanism in PCOS via measuring the protein expressions of apoptosis and anti-apoptosis related molecules in PCOS patients. A total of 30 PCOS patients were recruited in the disease group, in parallel with uterine fibroids patients as control group. TUNEL assay was used to determine the apoptotic index of ovary follicular granule cells. Immunohistochemistry (IHC) staining was performed to test the expressions of Bcl-2, Bax, Fas and Fas-L in various grades of follicular granules. PCOS group had higher apoptosis index of antral follicles compare to those in preantral follicles or primordial follicle (P<0.05). With time elapse, apoptosis index was gradually increased. PCOS group had higher apoptosis index in all grades of follicles compared with control group at the same time (P<0.05). Antral follicle had depressed Bcl-2 expression, and elevated Bax, Fas and Fas- L expressions compared with pre-antral, primordial follicles (P<0.05), or even control group (P<0.05). With time elapse, Bcl-2 expression was further decreased with elevated Bax, Fas and Fas-L expression in PCOS group (P<0.05). PCOS patients had elevated apoptosis of follicular granular cells, possibly resulting from down-regulation of Bcl-2 and up-regulation of Bax, Fas and Fas-L.