Recent data suggest that both nocturnal and diurnal mammals generate circadian rhythms using similarly phased feedback loops involving Period genes in the suprachiasmatic nucleus (SCN) of the hypothalamus. These molecular oscillations also exist in the brain outside of the SCN, but the relationship between SCN and extra-SCN oscillations is unclear. We hypothesized that a comparison of "diurnal" and "nocturnal" central nervous system Per rhythms would uncover differences in the underlying circadian mechanisms between these two chronotypes. Therefore, this study compared the 24 h oscillatory patterns of Per1 and Per2 mRNA in the SCN, and putative striatum and cortex of Octodon degus (degu), a diurnal hystricognath rodent, with those of the nocturnal laboratory rat, Rattus norvegicus. The brains of adult male degus and rats were collected at 2 h intervals across 24 h in entrained light:dark and constant darkness conditions, and sections were analyzed via in situ hybridization. In the SCN, degu Per1 and Per2 hybridization signal exhibited 24 h oscillatory patterns similar in phasing to those seen in other rodents, with peaks occurring during the light period and troughs during the dark period. However, Per1 remained elevated for five fewer hours in the degu than in the rat, and Per2 remained elevated for 2 fewer hours in the degu. In brain areas outside of the SCN, the phase of Per2 hybridization signal rhythms in the degu were 180° out of phase with those found in the rat, and Per1 hybridization signal lacked significant rhythmicity. These results suggest that while certain basic components of the transcriptional-translational feedback loop generating circadian rhythms are similar in diurnal and nocturnal mammals, there are variations that may reflect adaptations to circadian niche.