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The master circadian clock in mammals is the suprachiasmatic nucleus of the hypothalamus (SCN). The SCN generates sustained 24 hour rhythms of molecular oscillation and electrical activity, entrains to light, and synchronizes peripheral tissues. The molecular mechanisms involved SCN cell type specific function, rhythm generation, and signaling to and from the periphery remain incompletely understood. To address basic SCN function, we profiled its RNA expression at 2-hour resolution over 48 hours using Affymetrix 1.0ST arrays. We found ~500 cycling transcripts. These data offer crucial insight into circadian regulation of neuronal connectivity, synaptic transmission, ion homeostasis, splicing factors and protein-folding chaperones. We studied the circadian clock’s response to metabolic perturbations using control, low protein (LP), or high fat (HF) in utero diet during gestation and weaning. We also studied interaction of in utero and adult diet in mice given a control or LP in utero diet followed by a control or HF adult diet. Adult mice from all diet conditions were analyzed for circadian locomotor activity (tau) using running wheels. Adult HF diet had a greater effect than HF in utero diet of lengthening tau in both male and female mice. LP in utero diet lengthened tau in male mice, but did not affect female mice. Circadian CNS response to these in utero and adult diet conditions was measured using PER2::LUCIFERASE expression in the SCN and a neighboring hypothalamic nucleus regulating feeding and satiety, the arcuate nucleus. Period length of PER2::LUC was not affected by diet in the SCN, but both male and female mice exhibited trends of lowered baseline and amplitude of PER2::LUC in all dietary perturbation conditions compared with controls. In the arcuate, dietary perturbations showed trends of increasing baseline and amplitude of PER2::LUC in male mice, while the opposite effect was seen in females. Overall, our data show extensive circadian regulation of gene