Claudins (CLDNs) are transmembrane proteins, as normal constituents of the architecture of tight junctions. Recent studies support their involvement in carcinogenesis, as changes in CLDNs structure result in alterations in tight junctions' structure and function, facilitating malignant transformation. We aimed CLDN3 investigation in both breast and ovarian carcinoma, targeting the identification of its expression differences. The immunohistochemical assessment was performed on 20 cases of breast carcinomas (Group 1) and 19 cases of epithelial ovarian carcinomas (Group 2). Firstly, the specific panel for the molecular classification was applied for specimens of the first group. Then, all the specimens were immunostained for CLDN3 and a semi-quantitative evaluation was made, based on the percentage of positive cells and the intensity of staining. In Group 1, in the ER positive category, CLDN3 was overexpressed in five cases (four cases of luminal A and one case of luminal B subtype, respectively), negative in three cases (luminal A subtype) and weakly expressed in a single case (luminal A subtype); in ER negative category, CLDN3 expression was strong in four cases (one case of Her2/neu subtype and three cases of basal-like subtype), negative in two cases (normal breast-like subtype) and weak in five cases (one case of Her2/neu subtype, one triple-negative subtype, and three basal-like subtype). In Group 2, CLDN3 was overexpressed in 15 cases, histopathologically diagnosed as serous (10 cases), mucinous (two cases), endometrioid (two cases), and mixed carcinomas (one case); a weak expression was noticed in a single case, of the serous subtype; CLDN3 was undetectable in three cases (one serous, one clear cell, and one endometrioid type). Our comparative analysis of CLDN3 profile in breast and ovarian cancer clearly indicates organ specificity.