The three chromosomal translocations t (11; 18)(q21; q21), t (14; 18)(q32; q21), and t (1; 14)(p22; q32) are associated with MALT lymphoma. In a case of MALT lymphoma of the thyroid, we observed t (3; 14)(p14. 1; q32) by cytogenetic analysis. Fluorescence in situ hybridization studies showed that the immunoglobulin heavy chain locus (IGH) was rearranged on chromosome 14. Long-distance inverse polymerase chain reaction identified FOXP1 as the partner gene on chromosome 3. To determine the frequency of the t (3; 14)(p14. 1; q32), two fluorescence in situ hybridization assays were established to screen 91 MALT lymphomas, all of which were negative for the above-mentioned three translocations, and eight splenic and six nodal marginal zone lymphomas. Overall, nine MALT lymphomas (10%) harbored t (3; 14)(p14. 1; q32) comprising tumors of the thyroid (three of six), ocular adnexa (four of 20), and skin (two of 20), whereas those of the stomach (n= 20), salivary gland (n= 20), and lung (n= 5) were negative as well as the splenic and nodal marginal zone lymphomas. Most t (3; 14)(p14. 1; q32)+ MALT lymphomas harbored additional genetic abnormalities, such as trisomy 3. Further studies revealed that the three known translocations and t (3; 14)(p14. 1; q32) are mutually exclusive. Real-time quantitative reverse transcriptase polymerase chain reaction showed upregulation of FOXP1 in cases with t (3; 14)(p14. 1; q32) or trisomy 3. This study identifies FOXP1 as a new translocation partner of IGH in a site-dependent subset of MALT lymphomas.