PURPOSE To determine whether molecular genetic analysis of ocular-adnexal lymphoid tumors, combined with histopathology and tumor location, is helpful in predicting which patients will develop systemic lymphoma. METHODS A combined retrospective and prospective study of 77 patients with ocular-adnexal lymphoid tumors was performed. The tumors were subdivided into conjunctival, orbital, and eyelid lesions, and all were studied using both routine histopathology and molecular genetic analysis. RESULTS Most lesions (70%) were small cell lymphomas of the mucosa-associated lymphoid tissue type, and the majority of tumors (90%) contained monoclonal or oligoclonal populations of lymphocytes discovered on molecular genetic analysis. Additionally, 72% of tumors exhibiting clonality had more than one gene rearrangement. Fifty-three percent of patients developed extraocular lymphoma sometime during the course of their disease. Patients with gene rearrangements on Southern blot hybridization had a 52% incidence of nonocular disease, compared with 63% of those without rearrangements. Patients with conjunctival tumors had a 37.5% incidence of nonocular disease, those with orbital tumors had a 54% incidence, and those with eyelid tumors had a 100% incidence of nonocular lymphoma. Only two patients died as result of systemic lymphoma. CONCLUSIONS Most ocular-adnexal lymphoid tumors are lymphomas of the mucosa-associated lymphoid tissue type. The majority of tumors exhibit gene rearrangements on molecular genetic analysis, and this technique was not helpful in predicting which patients would develop nonocular lymphoma. Tumor location did have predictive value: Conjunctival lesions had the lowest incidence of nonocular lymphoma, and lid lesions had the highest incidence. Even with disseminated disease, most patients have a favorable prognosis with treatment.