This study aimed to investigate the clinical significances of phosphatase and tension homology deleted on chromosome ten (PTEN) and human epidermal growth factor receptor 2 (HER-2) protein expression in endometriosis associated ovarian carcinomas (EAOC) and their correlations. Seventy-eight cases of EAOC specimen and 60 cases of ovarian endometrial cyst (OEC) specimen were collected. The expressions of PTEN and HER-2 protein were determined using immunohistochemical analysis. Their relationships with clinicopathological features of EAOC and their correlations were analyzed. Results showed that, in 78 cases of EAOC, the expression level of PTEN protein in EAOC tissues was significantly lower than that in OEC tissues (P<0.01), and that of HER-2 protein in EAOC tissues was significantly higher than that in OEC tissues (P<0.01). The positive rates of PTEN and HER-2 protein had significant difference between EAOC with FIGO stage I-II and III-IV (P<0.01) and between EAOC with G1-G2 and G3 differentiation (P<0.01), respectively. In EAOC the expressions of PTEN and HER-2 protein were negatively correlated (r=-0.714, P<0.001). In conclusion, the expressions PTEN and HER-2 protein are significantly related to the FIGO stage and differentiation grade of EAOC, and they are negatively correlated.