OBJECTIVE To study the diagnosis and classification of ocular adnexal lymphoid hyperplasia and investigate its cell origin by using some molecular biological techniques. METHODS 29 cases (31 eyes) of ocular adnexal lymphoid hyperplasia were examined for immunoglobulin heavy-chain (IgH) gene rearrangements by means of polymerase chain reaction (PCR) to amplify the complementarity determining region III (CDR-III) with formalin-fixed and paraffin-embedded tissue combining with histopathologic examination and immunophenotypic analysis. RESULTS 17 eyes of malignant lymphoma and 5 eyes of reactive lymphoid hyperplasia demonstrated clear single band of the rearranged gene for the IgH chain between 100 bp. to 120 bp. The bilateral ocular adnexal lymphoma occurring simultaneously in 4 eyes (two individuals) exhibited identical band. 1 eye of malignant lymphoma, 8 eyes of atypical lymphoid hyperplasias and 6 eyes of reactive lymphoid hyperplasia showed no band or a smear band. CONCLUSIONS The results show that this method can determine the clonality of the lymphoid hyperplasias. It may be as well in the examination of small monoclonal B cell populations for which immunophenotypical analysis is difficult. The method is an objective, accurate and useful approach for the diagnosis of ocular adnexal lymphoid hyperplasias.