Ovarian clear cell carcinomas (CCC) typically present as large adnexal, stage I tumors and are generally considered highly malignant. They are frequently associated with endometriosis and, less often with clear cell adenofibromas. We hypothesized that CCCs are a heterogeneous group of tumors, some arising from a cyst and others from an adenofibroma. To test this hypothesis, 122 cases of CCC were retrieved from the surgical pathology files of National Taiwan University Hospital (74), The Johns Hopkins Hospital (23), and Serei Mikatahara General Hospital (23) (1985 to 2006). Cases were divided into 3 subgroups: (1) cystic, (2) adenofibromatous, and (3) indeterminate. Various features were analyzed including: age, race, laterality, tumor size, architectural pattern (papillary, tubulo-cystic, solid, mixed patterns), grade, mitotic index, association with endometriosis including atypical endometriosis/intraepithelial carcinoma, stage and survival. Nearly 70% of all the patients were diagnosed as stage I. The 2-year and 5-year survival (all stages) was 78% and 68%, respectively. Striking clinicopathologic differences were observed between cystic and adenofibromatous CCCs. Cystic CCC was more frequently diagnosed as stage I compared with adenofibromatous CCC (75% vs. 44%). Conversely, adenofibromatous CCCs were diagnosed more often in advanced stages (stages II-IV) compared with cystic CCCs (56% vs. 18%). Both the cystic and adenofibromatous CCC forms were associated with endometriosis and atypical endometriosis/intraepithelial carcinoma, but the frequency was much higher in the cystic group. Specifically, endometriosis was found in 91% of cystic CCCs and atypical endometriosis/intraepithelial carcinoma in 62% of these cases, whereas endometriosis was found in 44% of adenofibromatous CCCs and atypical endometriosis/intraepithelial carcinoma in 11% of cases. A predominantly papillary pattern was seen in 47% of cystic CCCs, whereas none of the adenofibromatous carcinomas displayed a predominantly papillary pattern. A more favorable outcome was observed for cystic CCCs compared with adenofibromatous CCCs (all stages) which was accounted for by the high proportion of stage I tumors. The 2-year and 5-year survival for the cystic CCCs was 82% and 77% and for the adenofibromatous CCCs (all stages), 62% and 37%, respectively. In summary, subdividing ovarian CCCs into cystic and adenofibromatous CCC reveals differences in a number of clinicopathologic features including their association with endometriosis, histologic patterns, stage distribution, and clinical behavior. Because there were a relatively small number of adenofibromatous CCCs in this series, additional cases must be studied to confirm these findings.