The suprachiasmatic nuclei (SCN) of the hypothalamus are necessary for coordination of major aspects of circadian rhythmicity in mammals. Although the molecular clock mechanism of the SCN has been a field of intense research during the last decade, the role of the neuropeptides in the SCN, including arginine-vasopressin (AVP), vasoactive intestinal polypeptide (VIP) and gastrin-releasing peptide (GRP), in the clock itself or in circadian organization is still largely unknown. Previous studies mainly performed in the rat have examined the profiles of AVP, VIP and GRP mRNA and peptide levels and suggested that the AVP rhythm is controlled by the circadian clock, whereas those of VIP and GRP are directly dependent on lighting conditions. Here, both daily (i.e., under light-dark cycle [LD]) and circadian (i.e., in constant darkness [DD]) profiles of neuropeptide mRNA were investigated in the SCN of the nocturnal mouse Mus musculus and the diurnal rodent Arvicanthis ansorgei to gain insight into a possible role in circadian organization. Our data show that AVP mRNA exhibits a clear circadian rhythm in the SCN peaking by the end of the subjective day in both species. Contrary to what has been observed in rats, oscillations of VIP and GRP mRNA in the SCN are found to be clock-controlled in mice and A. ansorgei, but with different phases for peak expression. While both VIP and GRP mRNA peak during the middle of the subjective night (i.e., with a 6-h lag compared to AVP mRNA) in mice, they peak almost in phase with AVP mRNA in A. ansorgei. Contrary to what has been reported in the rat, mean levels of VIP and GRP peptide mRNA levels tended to be increased by light in the mice. The different circadian organization of SCN neuropeptides mRNA profiles in both light/dark and constant darkness conditions between mice and A. ansorgei could be related with diurnality.