In the present work we analyze by reverse transcription, polymerase chain reaction, cDNA cloning, and sequence analysis the expression of membrane melatonin receptors in rat thymus and spleen. Results show, for the first time, that the melatonin receptor mRNA is expressed in both the thymus and spleen. Moreover, the melatonin receptor mRNA was expressed in all the lymphocyte subpopulations (CD4⁺, CD8⁺, double positive, double negative, and B cells) studied from the rat thymus. The Southern blot analysis with the melatonin receptor probe and sequence data also showed the identity of the DNA fragments in thymus, spleen, and the lymphocyte subpopulations studied. The melatonin receptor fragments amplified from rat brain, thymus, and spleen share identical nucleotide sequences with the rat Mel_la‐melatonin receptor subtype. No signal was obtained with primers used to amplify the rat Mel_1b‐melatonin receptor subtype in both thymus and spleen. Finally, the melatonin receptor mRNA transcript distribution throughout the rat thymus was examined. Using digoxigenin‐labeled cRNA probe to the specific melatonin receptor mRNA, examination of the whole thymus revealed a clear hybridization signal in both cortex and medulla. Melatonin receptor gene expression in the thymus and spleen supports the notion of the immunomodulatory role of melatonin.—Pozo, D., Delgado, M., Fernandez‐Santos, J. M., Calvo, J. R., Gomariz, R. P., Martin‐Lacave, I., Ortiz, G. G., Guerrero, J. M. Expression of the Mel_1a‐melatonin receptor mRNA in T and B subsets of lymphocytes from rat thymus and spleen. FASEB J. 11, 466–473 (1997)