While the site of the major circadian pacemaker in mammals, the suprachiasmatic nucleus (SCN) of the hypothalamus, is very well characterized, little is known about hypothalamic circadian organization in birds. This paper reviews recent findings on clock gene expression in the hypothalamus of several bird species focusing on circadian pPer2 expression in the house sparrow. In contrast to mammals, rhythmic Per2 gene expression in the house sparrow hypothalamus is not restricted to a single cell group but occurs in two distinct hypothalamic nuclei, the SCN and the lateral hypothalamic nucleus (LHN). The complex temporal and spatial distribution of pPer2 expression suggests a longitudinal compartmentalization of the SCN with period gene expression being initiated in the most rostral portion before lights on. In the lateral hypothalamus, phasing of pPer2-rhythmicity appeared delayed. In pinealectomized house sparrows, the overall circadian pPer2 expression pattern is maintained indicating that rhythmic pPer2 transcription in the SCN and LHN of the house sparrow are not driven by the pineal gland. Rather, they reflect the activity of autonomous hypothalamic circadian oscillators. Certain changes in peak expression levels and the expression phase, however, suggest that the pineal melatonin rhythm affects both the phase and the amplitude of rhythmic hypothalamic pPer2 expression.