In mammals, two types of cryptochrome are involved in the regulation of the circadian rhythm. We previously characterized rat Cry2 and its expression in brain tissue [Eun et al. (2001)]. We report here the cloning of another cryptochrome gene, Cry1, from rat brain by reverse-transcription coupled to polymerase chain reaction (RT-PCR), together with rapid-amplification of cDNA ends (RACE). The cloned Cry1 cDNA consists of 2557 nucleotides and has a single open-reading frame encoding a protein of 588 amino acids with start and stop codons. The deduced amino acid sequence was 70% identical with that of rat Cry2. It also showed 95% identity with mouse and human Cry1 but relatively low identity of 82% with that of zebrafish. Circadian expression of rat Cry1 and Cry2 was examined in the suprachiasma nucleus (SCN) and eye by real-time PCR. Expression of Cry1 and Cry2 mRNA in the SCN displayed a circadian rhythm with a peak at the day/night transition, and there was a slightly different circadian pattern of expression of Cry1 and Cry2 in the eye.