The forkhead box protein P1 (FOXP1) expression resulted from chromosome translocation was found in MALT lymphoma, and its nuclear expression in diffuse large B cell lymphoma has been believed to be a poor prognostic factor. In our study, FOXP1 expression was investigated in its relationship to the occurrence of large tumor cells, clinical features, and prognosis in a series of 115 MALT lymphomas divided into two groups with or without the large tumor cells. All cases were morphologically reviewed, and FOXP1 expression was detected both in mRNA and protein levels by real-time PCR, immunochemical staining, and Western blot hybridization. All available clinical data were collected. In the MALT lymphoma with large cells, FOXP1 expression was higher at both mRNA (P = 0.008) and protein (P = 0.000) levels than that in group without large cells, and most large tumor cells showed FOXP1 positivity. It was also found that cases beyond Ann Arbor stage I have a higher FOXP1 expression rate than cases in stage I (P = 0.01), moreover, FOXP1-positive group has more plasmacytic differentiation (P = 0.025), deeper filtrating depth in digestive tract (P = 0.039), and a higher Ki67 proliferation index (P = 0.022). However, no statistical significance was identified in the involved anatomic sites and prognosis. Our data demonstrated the close relationship between FOXP1 nuclear expression and the occurrence of large tumor cells in MALT lymphoma, which suggested the possibility of large cell transformation of FOXP1-positive cases. And FOXP1 positivity was associated with enhanced invasion and proliferation ability of tumor cells. In the thyroid cases, the FOXP1 positivity showed a poorer prognosis (P = 0.043), but the significance was not found in the overall survival analysis (P = 0.1123).