Photoperiodism is an important adaptive phenomenon in various physiological parameters including reproduction to cope with seasonal changes. Involvement of extraretinal photoreceptors in the photoperiodism in non-mammalian vertebrates has been well established. In addition, circadian clock system is known to be involved in the photoperiodic time measurement. The pathway consists of light-input system, time measurement system (circadian clock), gonadotropin releasing hormone (GnRH) production in the hypothalamus, luteinizing hormone (LH) and follicle stimulating hormone (FSH) production in the pituitary, and final gonadal development. Recently, several laboratories reported photopigments newly cloned in the pineal, eyes and deep brain in addition to already known visual pigments in the retina. These are pinopsin, parapinopsin, VA-opsin, melanopsin, etc. All these photopigments belong to the opsin family having retinal as the chromophore. However, the function of these photopigments remains unknown. I reviewed the studies on the location of the photopigments by immunocytochemistry. I also discussed the results on the action spectra for induction of gonadal development in relation with the location of the photoreceptors. Various physiologically active substances distribute in the vertebrate brain. Such substances are GnRH, GnIH, neuropeptide Y, vasoactive intestinal peptide, c-Fos, galanin, neurosteroids, etc. I summarized the immunhistochemical studies on the distribution and the photoperiodic changes of these substances and discussed the route from the deep brain photoreceptor to GnRH cells.