We evaluated the diagnostic value of hepatocyte nuclear factor 1 beta (HNF-1β) and napsin A for diagnosing ovarian clear cell carcinoma. Immunohistochemical EnVision was used to measure HNF-1β and napsin A expression in 38 cases of ovarian clear cell carcinoma, 30 cases of high-grade serous carcinoma, 22 cases of endometrioid adenocarcinoma, and 16 metastatic Krukenberg tumor cases. Then we found that HNF-1β appeared in all ovarian clear cell carcinoma and was less common in high-grade serous and endometrioid adenocarcinoma (P 0.05). Napsin A was expressed in 97.4% of ovarian clear cell carcinoma, 6.7% high-grade serous carcinoma, 22.7% endometrioid adenocarcinoma, and 0% metastatic Krukenberg tumors. Napsin A in clear cell carcinoma was greater than that found in high-grade serous carcinoma, endometrioid adenocarcinoma, and metastatic Krukenberg tumor (P < 0.05). Sensitivity and specificity of HNF-1β and napsin A for diagnosing ovarian clear cell carcinoma was 100% and 54.4%, and 97.4% and 89.7%, respectively. Sensitivity and specificity of HNF-1β and napsin A for diagnosing ovarian clear cell carcinoma was 97.4% and 91.2%, respectively. So it is concluded that HNF-1β and napsin A are more sensitive than currently used markers for diagnosing ovarian clear cell carcinoma. Moreover, napsin A is more specific than HNF-1β. Combining HNF-1β and napsin A may distinguish clear cell carcinoma from high-grade serous carcinoma, endometrioid adenocarcinoma and metastatic Krukenberg tumors.