The suprachiasmatic nuclei (SCN) contain a circadian system consisting of circadian oscillator (clock) that is normally synchronized by the light/dark cycle (input) and drives circadian rhythms (output) that are intrinsic to the SCN. Gene expression of immediate-early genes, such as c-fos and jun-B, in the ventrolateral SCN is associated with circadian synchronization by light pulses and subjected to circadian control. Vasopressin and somatostatin gene expression shown distinct circadian rhythms intrinsic to the dorsomedial SCN with higher peptide levels occurring during the day. In addition, embryonic SCN grafted into the brain of an SCN-lesioned arrhythmic host define the period of the restored circadian locomotor rhythm. Taken together, these and other findings support the notion that the expression of genes underlying circadian synchronization, oscillation and output takes place within individual SCN neurons. However, no information regarding the nature and number of those neurons as well as the molecular mechanisms of the single cell-circadian oscillator and output is currently available. Therefore, we propose a simple two-neuron model as a framework for critically discussing the molecular genetic strategies to analyze the circadian system in SCN.