Extraretinal photoreceptor cells have been found in the pineal complex and deep brain of a variety of non-mammalian vertebrates. Light signals received by these photoreceptor cells seem to be a potent regulator of diverse physiological responses. Here, the pineal complex and deep brain of the Japanese grass lizard, Takydromus tachydromoides, were immunohistochemically analyzed to localize the photoreceptive molecule (opsin) and the light signal-transducing G-protein (transducin). In addition to the pineal organ and parietal eye constituting the pineal complex, we unexpectedly found a parapineal organ, which is located just below the parietal eye and is morphologically similar to the pineal organ. Both organs had photoreceptor-like cells with outer segments immunostained by anti-rhodopsin and anti-pinopsin antibodies. Neither opsin- nor transducin-like immunoreactivities were detected in the parietal eye with all the antibodies tested in this study, although its morphology resembles that of the lateral eyes. In the deep brain region, rhodopsin-like immunoreactivities were observed in the posterior pallial commissure and median eminence. The cerebrospinal fluid-contacting neurons in the paraventricular organ were immunoreactive to an antibody against α-subunit of cone transducin. In lizards, this is the first report showing (1) rhodopsin- and pinopsin-like immunoreactivities in the parapineal organ, (2) rhodopsin-like immunoreactivity in the deep brain, and (3) putative photoreceptive areas in the hypothalamus.