Primary orbital non-Hodgkin lymphoma is a mucosa-associated lymphoid tissue (MALT)-type extranodal marginal zone lymphoma. Little information is available on its genome as conventional cytogenetics is limited by scarce biopsy material, while fluorescence in situ hybridization (FISH) explores only selected regions. Comparative genomic hybridization (CGH) performs full genomic analysis and is applicable to different sources of DNA, such as fresh and frozen cells, as well as paraffin-embedded tissues. In this study, CGH was used to analyse primary MALT lymphoma of the orbit. Aneuploidy was identified in six of the ten cases studied. Gains (19) were more frequent than losses (5). The most frequent duplications involved chromosome 3 (common region at 3q24-qter), as expected in marginal zone lymphoma, and chromosome 6 (common region at 6p21.1-21.3), which is typical of an orbital location. Other chromosome gains were found at 1p, 7, 8q, 9q, 12, 13, 17, 18, 19, 22, and X. Losses were located at 1q, 6q, 9q, 11q, and 13q. Two cases showed isolated duplications of chromosome 6p or 9q. Isolated imbalances were found only in tumours affecting the conjunctiva. Complex aneuploidies were observed in lymphoma of the retro-orbital tissue. In summary, CGH in orbital MALT lymphoma provided new insights into typical genomic imbalances and underlying pathogenetic mechanisms.