Objective To investigate the expression of claudin-3 and β-catenin in borderline ovarian tumors (BOTs) and its clinicopathological significance. Methods We examined the expressions of claudin-3 and β-catenin and their relationship with the clinicopathological features in 17 normal ovarian tissues, 31 epithelial benign ovarian tumors, 39 epithelial malignant ovarian tumors and 69 BOTs by SP immunohistochemistry method. Results The positive expression rate of claudin-3 protein in BOTs (59.4%, 41/69) was significantly lower than that in the malignant ovarian tumors (89.7%, 35/39), and higher than that in normal ovaries (5.9%, 1/17) and benign ovarian tumors (22.6%, 7/31)(P<0.01); the expressions were not significantly different between the normal ovaries and benign ovarian tumors (P>0.05). The positive expression rate of β-catenin protein in BOTs (52.2%, 36/39) was significantly lower than that in the malignant ovarian tumors (84.7%, 33/39), and higher than that in normal ovaries (11.8%, 2/17) and benign ovarian tumors (29.0%, 9/31; P<0.01 or P<0.05); the expressions were not significantly different between the normal ovaries and benign ovarian tumors (P>0.05).The expression of claudin-3 and β-catenin was correlated with the clinciopathological stage and intraperitoneal metastases (P<0.05), but not with the histological type or age of BOTs patients (P>0.05). Expression of claudin-3 and β-catenin was positively correlated in BOTs (r=0.439, P=0.000). Conclusion Claudin-3 and β-catenin may play a synergistic role in the oncogenesis and progression of BOTs. Simutaneous detection of claudin-3 and β-catenin is valuable for diagnosis and treatment of BOTs.