The high rate of mortality associated with ovarian cancer (OC) is due in part to the development of resistance to chemotherapy, which allows the resistant tumour cells to invade and metastasise. Clarifying the mechanistic basis for drug resistance may reveal novel avenues for treatment. The present study investigated the mechanism of paclitaxel (PTX) resistance in human epithelial OC by evaluating the expression of stem cell-associated cell surface markers endoglin (CD105), CD44 antigen and vascular cell adhesion molecule 1 (CD106), in association with the malignant potential of the human OC OVCAR3 cell line and its PTX-resistant derivative OC3/TAX300. The expression of CD105, CD44 and CD106 was detected by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and flow cytometry, and cell invasion was evaluated using a Transwell invasion assay. CD105, CD44 and CD106 levels were increased in OC3/TAX300 cells compared with the OVCAR3 cells, as determined by flow cytometry (P<0.01) and RT-qPCR (P<0.05). Additionally, the number of invading cells was increased in the OC3/TAX300 group compared with the OVCAR3 group (54.7±6.65 vs. 31.8±6.55; P<0.01). A western blot analysis of cell surface marker expression in 80 clinical epithelial OC tissue samples, differing in terms of sensitivity to drug treatments, disease stage and degree of differentiation, revealed that high CD105, CD44 or CD106 expression was associated with drug resistance, advanced disease stage, poor differentiation and high rate of recurrence. These data indicated that exposure to high doses of PTX enhanced the stem-like properties of OC cells, which are associated with drug resistance and invasion and lead to poor prognosis due to induced chemoresistance and/or metastasis. Therefore, CD105, CD44 and CD106 may serve as potential stem cell-associated cell surface and prognostic markers, and therapeutic targets, in OC.