Introduction: Failure of effective treatment of epithelial carcinoma of the ovary necessitates searching factors that lead to resistance to chemotherapy and recurrence. Cancer stem cell theory hypothesis provides an explanation of how small group of cells inside the tumour remain resistant to treatment. CD44 has been considered as cancer stem cell marker in multiple malignancies but its role in Ovarian Serous Carcinoma (OSC) is still controversial. Aim: To investigate the expression of stem cell marker CD44 and proliferative activity using Ki67 immunostaining in serous ovarian carcinoma and their relation to clinical and pathological variables and outcome of the patients. Materials and Methods: The present study was a prospective study done on 45 patients with serous ovarian tumours, the ovarian sections obtained from the patients were immunostained by CD44 and Ki67 immunohistochemical markers. The Overall Survival (OS), Disease Free Survival (DFS) and response to treatment were investigated and analysed. Results: Both CD44 and Ki67 were positive in patients with increased grade and advanced stage and the difference was highly statistically significant (p=0.001 and p<0.001, respectively). CD44 and Ki67 expression were higher in bilateral cancer with presence of lymph node and distant metastasis than in unilateral tumours without lymph node and distant metastasis. The present study found positive relation between CD44 and Ki67 expression (p=0.006). CD44 and Ki67 positive expression level in OSC had a significantly shorter 3-year DFS than the patient group with negative expression of CD44 and Ki67 (p=0.020 and p=0.002, respectively). Conclusion: This study demonstrated that CD44 and Ki67 expression were significantly associated with high grade and late stage serous ovarian carcinoma, and their high expression was associated with poor prognosis and resistance to chemotherapy, so proper quantification may play a vital promising function in choosing targeting therapy and predicting more better result outcome.