Abstract Vasoactive intestinal peptide (VIP) and neuropeptide Y (NPY) content in the suprachiasmatic nucleus have been shown to exhibit seasonal changes with an increase in late summer, the period of sexual quiescence in the jerboa ( Jaculus orientalis). In this study, VIP content in the SCN and NPY and enkephaline (ENK) content in the geniculo-suprachiasmatic system have been assayed in wild-caught male jerboas ( Jaculus orientalis) in order to determine whether these neuropeptides are controlled directly by photoperiod changes or indirectly by short photoperiod induced changes in circulating sex hormones levels. In agreement with previous studies seasonal variations occur in the VIP and NPY content in the SCN. Variations also occur in NPY content in the IGL with an increase in the period of sexual quiescence. In contrast, no seasonal changes are observed in Enk content in the IGL or the SCN. In short photoperiod conditions increases are observed in both VIP and NPY content in the SCN as well as NPY content in the IGL. Castration during the period of sexual activity (spring) or under long photoperiod which drastically reduces testosterone, also induced an increase in the levels of these neuropeptides. Testosterone implants which reproduce the sex hormonal status of the sexual activity period failed to prevent the short photoperiod-induced increase of VIP and NPY in the SCN and of NPY in the IGL. These results clearly show that the photoperiod modulates VIP and NPY in the geniculo-suprachiasmatic system both by testosterone-linked and testosterone-independent mechanisms.