The mammalian retina contains an autonomous circadian oscillator that can sustain rhythms in outer segment disc shedding and melatonin synthesis even in the absence of cues from the central oscillator in the suprachiasmatic nucleus (SCN). The present investigation aimed to ascertain whether the steady-state levels of rod and cone opsin mRNA exhibited a circadian oscillation in the mouse, and if so, to characterise this oscillation with regard to phase. Retinas were collected from mice free-running in constant darkness at circadian times (CT) 0, 4, 12, 16, and 20. RNA was extracted for the production of Northern blots, which were sequentially hybridised with probes for alpha-tubulin (control), ultraviolet opsin, and rhodopsin. Whereas no significant oscillation was detected in the levels of alpha-tubulin, the levels of both ultraviolet opsin and rhodopsin transcripts oscillated with an amplitude of at least 3-fold. The highest levels were found at around CT12 (which corresponds to the subjective evening, the time of activity onset in the mouse). These results show that the levels of rod and cone photopigment mRNA are under circadian control. The significance of the rhythms and their phasing is discussed. These findings have potential clinical implications both with regard to nocturnal light treatment of phase asynchrony, and in the timing of chemo- and radiotherapy.