To describe recent advances in the understanding of the pathogenesis of the most common malignant lymphomas that occur as primary and secondary tumors in ocular tissues.Advances have been made in the understanding of the genetic alterations in mucosa-associated lymphoid tissue lymphomas, including various chromosomal translocations, such as the most recently described t(3;14)(p14.1;q32) involving the FOXP1 gene. Further, the development of ocular adnexal mucosa-associated lymphoid tissue lymphomas has been associated with Chlamydia psittaci in some geographic areas. Subdivision of diffuse large B-cell lymphoma into clinically prognostic groups had been achieved on the basis of gene expression profiles using complementary DNA microarrays. Tumor-infiltrating cells, such as macrophages, have been demonstrated to be of prognostic significance in follicular lymphoma.Understanding of the ocular adnexal and intraocular lymphomas has advanced with progress in lymphoma classification systems, namely the World Health Organization lymphoma classification. This knowledge is being fine tuned with advances in technology, such as complementary DNA microarrays. The clinical significance of this scientific progress has yet to be determined.