Period 2 (Per2) is an important clock gene involved in the regulation of the major circadian clock in the mammalian central nervous system, the suprachiasmatic nucleus. In addition, Per2 is expressed in many other stress-sensitive brain structures. We have previously showed that the non-preganglionic Edinger-Westphal nucleus (npEW) is the main site of the corticotropin-releasing factor peptide family member urocortin 1 (Ucn1) and that this peptide undergoes conspicuous expression changes in response to various stressors. Here, we hypothesized that in the rat npEW both Per2 and Ucn1 would be produced in a diurnal, rhythmical fashion. This hypothesis was tested by following this expected rhythm on two days in rats killed at four time points each day (Zeitgeber times 0, 6, 12, and 18). We showed the co-existence of Per2 and Ucn1 in the npEW with double-label immunofluorescence and demonstrated with quantitative RT-PCR and semi-quantitative immunocytochemistry diurnal rhythms in Per2 mRNA expression and Per2 protein content, each on a single different day, with a minimum at lights-off and a maximum at lights-on. We furthermore revealed a diurnal rhythm in the number of Ucn1-immunopositive neurones and in their Ucn1 peptide content, with a minimum at night and at the beginning of the light period and a peak at lights-off, while the Ucn1 mRNA content paralleled the Per2 mRNA rhythm. The rhythms were accompanied by a diurnal rhythm in plasma corticosterone concentration. Our results are in line with the hypothesis that both Per2 and Ucn1 in the rat npEW are produced in a diurnal fashion, a phenomenon that may be relevant for the regulation of the diurnal rhythm in the stress response.