Hypothalamic energy balance genes have been examined in the context of seasonal body weight regulation in Siberian hamsters. Most of these long photoperiod (LD)/short photoperiod (SD) comparisons have been of tissues collected at a single point in the light-dark cycle. We examined the diurnal expression profile of hypothalamic genes in hamsters killed at 3 h intervals throughout the light-dark cycle after 12 weeks housing in LD or SD. Gene expression of neuropeptide Y (NPY), agouti-related peptide (AGRP), proopiomelanocortin (POMC), cocaine- and amphetamine-regulated transcript (CART), long form leptin receptor (OB-Rb), suppressor of cytokine signaling-3 (SOCS-3), melanocortin-3 receptor (MC3-R), melanocortin-4 receptor (MC4-R), and the clock gene, Per 1, as control, were measured by in situ hybridisation in hypothalamic nuclei. Effects of photoperiod on gene expression and leptin levels were generally consistent with previous reports. Clear diurnal variation was observed for Per 1 in the suprachiasmatic nucleus (SCN) in both photoperiods. Temporal effects on expression of energy balance genes were restricted to OB-Rb in the arcuate nucleus (ARC) and ventromedial nucleus (VMH), where similar diurnal expression profiles were observed, and MC4-R in the paraventricular nucleus (PVN); these effects were only observed in LD hamsters. There was no variation in serum leptin concentration. The 24-hour profiles of hypothalamic energy balance gene expression broadly confirm photoperiodic differences that were observed previously based on single time point comparisons, and support the growing consensus that these genes have a limited role in seasonal body weight regulation, and further suggest limited involvement in daily rhythms of food intake.