The objective of this study was to analyze the expression and potential clinical role of cancer stem cell (CSC) markers in malignant ovarian germ cell tumors (MOGCT). CD34, CD44, and SOX2 protein expression by immunohistochemistry was analyzed in 49 MOGCT from patients treated in Norway during the period 1980-2011. Expression was analyzed for association with tumor type and clinicopathologic parameters. Tumors were diagnosed as dysgerminoma (DG; n=15), immature teratoma (IT; n=15), yolk sac tumor (YST; n=12), embryonal carcinoma (n=2), and mixed MOGCT (n=5). Tumor cell CD34 expression was significantly more common in YST, whereas stromal expression was only seen in IT (both P<0.001). CD44 was infrequently expressed, most often focally, in tumor cells, particularly in YST (P=0.026). CD44 was widely expressed in leukocytes, most prominently in DG. SOX2 was most frequently expressed in IT, with predominantly focal expression in some YST and uniform absence in DG (P<0.001). Stromal CD34 (P=0.012) and tumor cell SOX2 expression (P=0.004) were negatively associated with the involvement of the ovarian surface, presumably due to the low incidence of this event in IT. No significant association was found between CSC marker expression and other clinicopathologic parameters, including age, laterality, tumor diameter, and FIGO stage. In conclusion, CSC markers are differentially expressed in various MOGCT types, suggesting differences in the regulation of cancer-related processes. Expression of CD34, CD44, and SOX2 does not appear to be associated with clinical parameters in this patient group.