We present a case whereby standard immunohistochemistry and flow cytometry studies for a conjunctival biopsy were unable to reliably differentiate between the two distinct pathological processes of benign reactive lymphoid hyperplasia from conjunctival lymphoma. A tissue diagnosis was only able to be conclusively attained after the application of immunoglobulin heavy chain rearrangement studies to the specimen. This is unusual and to our knowledge has not been previously expressed in the literature. Hence, the use of these further molecular studies may have great potential clinical implications in helping resolve such diagnostic dilemmas.