In this study, two circadian related centers, the suprachiasmatic nucleus (SCN) and the intergeniculate leaflet (IGL) were evaluated in respect to their cytoarchitecture, retinal afferents and chemical content of major cells and axon terminals in the rock cavy (Kerodon rupestris), a Brazilian rodent species. The rock cavy SCN is innervated in its ventral portion by terminals from the predominantly contralateral retina. It also contains vasopressin, vasoactive intestinal polypeptide and glutamic acid decarboxilase immunoreactive cell bodies and neuropeptide Y, serotonin and enkephalin immunopositive fibers and terminals and is marked by intense glial fibrillary acidic protein immunoreactivity. The IGL receives a predominantly contralateral retinal projection, contains neuropeptide Y and nitric oxide synthase-producing neurons and enkephalin immunopositive terminals and is characterized by dense GFAP immunoreactivity. This is the first report examining the neural circadian system in a crepuscular rodent species for which circadian properties have been described. The results are discussed comparing with what has been described for other species and in the context of the functional significance of these centers.