Two melatonin receptors (MT1 and MT2) have been cloned. A third melatonin binding site, MT3, is known with remarkable and distinct pharmacological properties. We previously reported the purification of MT3 and identified it as the enzyme dihydronicotinamide riboside:quinone reductase 2 (NQO2). To investigate the relationship between NQO2 and MT3, we generated a NQO2-/- mouse strain. These mice no longer present MT3 binding sites as measured with 2-[125I]-iodo, 5-methoxycarbonylamino-N-acetyltryptamine, the specific MT3 radioligand. These data establish NQO2 as part of the MT3 binding sites in vivo and resolve the matter of the nature of the third melatonin binding site.