In mammals, the major pacemaker controlling circadian rhythmicity is located in the hypothalamic suprachiasmatic nuclei which are characterized by specific molecular features including the expression of three homologues of the Drosophila clock gene period (per). Until now, no comparable structure has been unambiguously described in the brain of any non-mammalian vertebrate. We cloned the PAS-domain of the Per2 gene in the house sparrow (Passer domesticus), a model organism in circadian research. Hypothalamic expression of passerPer2 (pPer2) showed a marked diurnal rhythm in the suprachiasmatic nucleus, a cell group located in the anterior hypothalamus directly above the optic chiasm and adjacent to the third ventricle. Additionally, pPer2 was diurnally expressed in the lateral hypothalamus. This first demonstration of rhythmic clock gene expression in the hypothalamus of a non-mammalian vertebrate provides basic information for future research on the evolution of circadian pacemaking systems.