Ovarian primitive germ cell tumors (GCTs) are uncommon tumors and sometimes pose diagnostic challenges. Among them, yolk sac tumor (YST) poses the greatest diagnostic difficulty and can be mistaken for clear cell carcinoma (CCC). Current immunohistochemical markers such as alpha-fetoprotein (AFP), glypican-3, cytokeratin (CK) 7, and epithelial membrane antigen (EMA) used to distinguish YST from CCC lack adequate sensitivity and specificity. Here by immunohistochemistry, we investigated a novel marker SALL4 in 98 GCTs (29 YSTs, 18 dysgerminomas, 6 gonadoblastomas, 6 embryonal carcinomas, 15 immature and 12 mature teratomas, 7 carcinoid tumors, 3 strumal carcinoids, and 2 struma ovarii) with particular interest of exploring SALL4 to distinguish YST from CCC. One hundred sixty-three non-GCTs including 45 CCCs were also stained. We found that SALL4 is strongly positive in more than 90% tumor cells in all YSTs, dysgerminomas, gonadoblastomas, and embryonal carcinomas. Variable SALL4 staining is seen in 11 of 15 immature teratomas. All other GCTs included in this study are negative for SALL4. Except 3 CCCs with focal SALL4 staining (<15% tumor cells), SALL4 is negative in the remaining 160 non-GCTs. We also compared SALL4 with AFP, glypican-3, CK7, and EMA in all YSTs and CCCs. AFP and glypican-3 are positive in 24 (83%) and 20 (69%) YSTs, respectively, whereas 16 (35%) and 13(28%) CCCs show positive AFP and glypican-3 staining, respectively. Three (10%) and 4 (14%) YSTs show focal (<2% tumor cells) CK7 and EMA staining, respectively. CK7 and EMA are positive in all 45 CCCs but 3 (7%) and 1 (2%) cases show staining in less than 30% tumor cells, respectively. Our findings indicate that SALL4 is a novel sensitive and specific marker for ovarian primitive GCTs. SALL4 is particularly useful in distinguishing YST from CCC and better than AFP, glypican-3, CK7, and EMA.