Thymomas of the same histological subtype sometimes manifest different biological behaviors. Metastasis Tumor Antigen-2 (MTA2) is targeted by the transcriptional repressor Kaiso, the distribution which is thought to be modulated by p120catenin (p120ctn). It is currently unclear if expression of p120ctn, Kaiso, and MTA2 relates to the biological behavior of thymoma. P120ctn, Kaiso, and MTA2 expression were examined in 137 cases of thymoma, three cases of thymic carcinoma, and 18 paired autologous normal thymic tissues using immunohistochemistry, and correlation of these proteins with histological subtypes and clinical stages were analyzed. In normal thymic epithelial cells, p120ctn was expressed on the cell membrane but Kaiso and MTA2 were not detected. Membranous p120ctn expression was reduced in thymoma epithelial cells, while ectopic cytoplasmic expression was observed in 76.6 % (105/137) of the cases. Cytoplasmic Kaiso was detected in 69.3 % (95/137) and nuclear MTA2 was detected in 70.8 % (97/137) of the thymomas. There were good consistencies (Kappa = 0.559, 0.512, 0.652; all P < 0.001) and correlations (r = 0.733, 0.652, 0.708; all P < 0.001) between cytoplasmic p120ctn, cytoplasmic Kaiso, and nuclear MTA2 expression in thymomas. All three protein factors correlated with histological type and clinical stage in thymoma (P < 0.05). Specifically, cytoplasmic p120ctn and Kaiso expression and nuclear MTA2 expression were higher in high-risk (types B2 and B3) thymomas and Masaoka stage III/IV thymomas than low-risk (types A, AB, and B1) and stage I/II thymomas (both P < 0.001), respectively. Cytoplasmic p120ctn, cytoplasmic Kaiso, and nuclear MTA2 expression correlated directly with histological type and Masaoka stage and may thus be used as potential biomarkers to predict biological behavior of thymoma.