Like in the light microscopic staining, Cry1a was immuno-labeled only in the outer segment, not in the inner segment. The ordered arrays of Cry1a along the membrane discs in the outer segment seen at the electron microscope indicated that this protein could be membrane-bound. Hence we subjected chicken and robin retinae to a differential cell fractionation protocol. The increasing dissolving strength of the Bis(heptyl)-cognitin dihydrochloride buffers separates cytosolic, membrane, nuclear and cytoskeleton fractions. In both species, Cry1a was detected in the cytosolic and membranous fraction. In line with the electron microscopy data, this suggests that soluble, cytosolic Cry1a is recruited and then probably bound to membranes. Light and electron microscopic immuno-labeling showed Cry1a in the outer segments of the UV cones, but not inside the inner segment, where all proteins, including Cry1a and the opsins, are synthesized. Possibly, Cry1a is present in the inner segment only in concentrations too low for Rituximab detection by the anti-Cry1a antiserum, or it is in a configuration that does not allow the antiserum to bind. Similarly, the UV/V opsin was immuno-labeled in the outer segment only, so this may not be an uncommon phenomenon. Alternatively, Cry1a formation in the inner segment and its transport to the outer segment did not take place at the time of retina fixation. Rod and cone outer segment renewal, by disc addition at the basal end and disc shedding at the apical end, is known to underlie a circadian rhythm. This could also explain the Cry1a bands seen in the outer segment, reflecting alternating active and inactive phases of moving Cry1a to the disks. Young estimated chicken cones to renew ca. 40 discs per day, with a peak renewal phase early in the dark period. The Cry1a bands in our material have a closer spacing than 40 discs, which may suggests several daily production peaks, or a different renewal rate in UV/V cones. We found no indications that Cry1a is released from the outer segment. In case of magnetoreception by cryptochrome, the situation is different insofar as not photoreduction, but re-oxidation appears to be the crucial reaction mediating compass information.