Mucosa-associated lymphoid tissue (MALT) lymphoma arising in the thymus is a rare disorder that shows a strong association with autoimmune disease. Several MALT-lymphoma-specific and -associated chromosomal abnormalities, including t(11;18), t(14;18), t(1;14), trisomy 3 and trisomy 18, are known to occur. The former translocation results in apoptosis inhibitor 2 gene (API2)–MALT lymphoma-associated translocation 1 (MALT1) fusion. In this study, we examined 14 cases of thymic MALT lymphomas for API2–MALT1 fusion using multiplex reverse transcription polymerase chain reaction and looked for trisomy 3, trisomy 18 and abnormalities of MALT1 and IGH genes using fluorescence in situ hybridization. Thymic MALT lymphoma cases had a high frequency of trisomy 3 (7/14 cases), a very low incidence of trisomy 18 (1/14) and no detectable MALT1-associated (0/13) or IGH-associated (0/13) gene abnormalities including t(11;18). A review of the literature showed that the pattern of chromosomal aberrations in thymic MALT lymphoma was similar to those of thyroid and salivary gland MALT lymphomas. Although frequently detected, trisomy 3 was not associated with any of the clinicopathological factors analyzed, suggesting that trisomy 3 may play a role in lymphoma development. In conclusion, the present study showed that thymic MALT lymphoma has a characteristic pattern of chromosomal aberrations that may be similar to those of other autoimmune-associated MALT lymphomas.