The anatomy and physiology of the non-image forming visual system was investigated in a visually blind cone-rod homeobox gene (Crx) knock-out mouse (Crx(-)(/)(-)), which lacks the outer segments of the photoreceptors. We show that the suprachiasmatic nuclei (SCN) in the Crx(-/-) mouse exhibit morphology as in the wild type mouse. In addition, the SCN contain vasoactive intestinal peptide-, vasopressin-, and gastrin-releasing peptide-immunoreactive neurons as present in the wild type. Anterograde in vivo tracings from the retina of the Crx(-/-) and wild type mouse showed that the retinohypothalamic projection to the SCN and the central optic pathways were similar in both animals. Telemetric monitoring of the running activity and temperature revealed that both the Crx(-/-)and wild type mouse exhibited diurnal rhythms with a 24-h period, which could be phase changed by light. However, power spectral analysis revealed that both rhythms in the Crx(-/-) mouse were less robust than those in the wild type. The normal development of the SCN and the central visual pathways in the Crx(-/-) mouse suggests that a modulatory input from the photoreceptors in the peripheral retina to the retinal melanopsin neurons or the SCN may be necessary for a normal function of the non-image forming system of the mouse. However, a change in the SCN of the Crx(-/-) mouse might also explain the observed circadian differences between the knock out mouse and wild type mouse.