Circadian rhythms are internally generated circa 24 h rhythms. The phase of the circadian pacemaker in mammals can be adjusted by external stimuli such as the daily cycle of light, as well as by internal stimuli such as information related to the physiological and behavioral status of the organism, collectively called "non-photic stimuli". We review a large number of studies regarding photic-non-photic interactions on the circadian system, with special focus on two widely described neurotransmitters associated with non-photic input pathways: neuropeptide Y (NPY) and serotonin 5-HT. Both neurotransmitters are capable of phase advancing the master pacemaker oscillation when applied during the subjective day, as do several behavioral manipulations. Also, both are capable of inhibiting light-induced phase shifts during the subjective night, suggesting a dynamic interaction between photic and non-photic stimuli in the fine-tuning of the pacemaker function. Suppression of the NPYergic and/or serotonergic non-photic input pathways can in turn potentiate the phase-shifting effects of light. These findings pose new questions about the possibility of a physiological role for the dynamic interaction between photic and non-photic inputs. This might be particularly important in the case of circadian system adjustments under certain conditions, such as depression, shift work or jet lag.