The cancer stem cells (CSCs) represent a minority of tumor cells that are able to proliferate and self-renew and might be responsible for tumor initiation and maintenance. The CD133 and CD117 are the most commonly used markers for putative CSCs, especially for ovarian CSCs, but its clinical significance remains uncertain. The aim of this study was to compare the immunohistochemical expression of CD133 and CD117 in 69 primary ovarian serous carcinoma and peritoneal metastasis, and to examine their potential clinical role. CD133 expression was mainly seen in the apical/endoluminal cell surface of tumor cells and was found in 58% of carcinoma samples and 42% of metastasis. The median of CD133 positive cells in tumors was 1 (0.1-7) %, and in metastases was 0.55 (0.1-6) %. CD117 expression appeared as a cytoplasmic and/or membranous stain and was found in 81% of carcinoma samples and 77% of metastasis. The median of CD117 positive cells in tumors was 1 (0.1-8) %, and in metastases was 0.1 (0.1-6) %. Multivariate analysis showed that patients with high CD133 expression in tumor have significantly shorter time to progression and time to survival (P=0.004 and P=0.016, respectively). Patients with high CD117 expression in tumor have significantly shorter time to progression (P=0.034). Cox´s proportional hazards model identified expression of CD133 protein in tumor as independent prognostic factor. Our study indicates that the immunohistochemical assessment of CD133 and CD117 expression may have potential clinical value in predicting disease progression and prognosis in serous ovarian cancer. CD133 proved to be an independent prognostic factor in serous ovarian cancer patients.