Background: It remains unknown whether primary ocular adnexal MALT lymphoma is a homogenous disease, because there have been few reports on cytogenetic or molecular analysis of this disease.Patients and Methods: In 34 cases of ocular adnexal MALT lymphoma, we performed interphase fluorescence in situ hybridization (FISH) analysis to detect IgH/MALT1 and API2/MALT1 fusion genes. Aneuploidy of chromosome 3, 7, 12 and 18 was also identified using corresponding centromere probes. We defined trisomy when three centromeres were recognized in FISH analysis. Histopathologic features were reviewed and categorized according to the degree of plasma cell differentiation, monocytoid B cell feature, nodularity, abundance of reactive germinal centers, multikaryocytic cells, contaminated T cells, Duthcer bodies, and lymphoepithelial lesions (LELs). Correlations among FISH analysis, histopathologic features, and clinical data were analyzed.Results: FISH analysis showed 1 (3%) IgH/MALT1 fusion, 21 (62%) trisomy 3, 16 (47%) trisomy 18, and 3(9%) trisomy 7 cases. No cases showed API2/MALT1 fusion or trisomy 12. Existence of these cytogenetic change did not influence the degree of morphological features significantly, except for trisomy 18; Cases with trisomy 18 had significantly more abundant LEL cells, monocytoid B cells and residual reactive germinal centers, but less nodules, contaminated plasma cells and large cells. Cases with trisomy 18 showed distinct features of female dominance, younger age, and included more cases originated from conjunctiva. In total, five (15%) of 34 patients relapsed between 21 and 103 months, and all of them were found to have trisomy 18.Conclusions: Aneuploidy is found in a ceratin subset of ocular adnexal MALT lymphoma by FISH analysis. Cases with trisomy18 may make a distinct clinicopathlogic entity.