A rare case of primary mucosa-associated lymphoid tissue lymphoma (MALT) of the rectum is reported. A 56-yr-old man was referred to our hospital for further examination and treatment of rectal neoplasm. A physical examination and laboratory data showed no special abnormalities. However, endoscopic colorectal observation revealed multiple red and slightly elevated nodular lesions with erosive changes of the rectum. The lesions were composed of diffuse, small atypical lymphoid cells (i.e., centrocyte-like cells) and were stained with L26 and BCL-2 but not cyclin D1. Surface markers of cells obtained from biopsy specimens were CD5-, CD10-, CD19+, CD20+, kappa+, and lambda-. No BCL-2 gene rearrangement was observed. The clonal karyotype of t(11;18)(q21;q21) was observed in six of nine lymphoid cells. Trisomy was also identified two of 144 cells by fluorescence in situ hybridization. We report a rare case of the rectal MALT lymphoma bearing characteristic chromosomal aberrations; t(11;18)(q21;q21) and trisomy 3. We suggest that chromosomal analysis using biopsy specimens may be useful for the diagnosis of MALT lymphoma.