Objective To explore the association of expression of apoptosis-associated gene BAK and cFLIP with the biological behaviors in endometriosis. Methods The expression of BAK and cFLIP protein gene in eutopic and ectopic tissue samples from 40 cases with pathologically confirmed ovarian endometriosis and 40 cases with pathologically confirmed normal endometrium was detected by immunohistochemical method. Results ①The expression of BAK and cFLIP protein gene was found in three groups of different endometrial tissue. ②The expression of BAK protein gene was increased gradually in ectopic endometrial , eutopic endometrium and normal tissue and there was significantly difference between every two groups ,while cFLIP was contrary expressed (P <0.05); ③In normal endometrium, The expression of BAK protein gene in secretory phase was higher than that in proliferative phase (P < 0.05), while cFLIP was contrary expressed, in eutopic endometrium and ectopic endometrial tissue , The expression of BAK and cFLIP protein gene in secretive phase showed no statistically significant difierence with that in proliferative phase (P > 0.05). ④The expression of BAK protein gene in severe group (Ⅲ-Ⅳ period) is lower than mild group both in eutopic or ectopic endometrial tissues,while cFLIP was contrary expressed (P < 0.05). ⑤The expression of BAK and cFLIP was negatively correlated with each other in ectopic endometrium (r=-0.389,P< 0.05). Conclusion BAK and cFLIP was negatively expressed in EMS, which may take a part in the endometrial apoptosis and disorderly proliferation. BAK and cFLIP may play an important role in the the diagnosis and treatment of endometriosis.