We performed a broad-scale screening of differential gene expression using both high-throughput beadarray technology and real-time PCR assay in brown adipose tissue, liver, heart, hypothalamus, and skeletal muscle in hibernating arctic ground squirrels, comparing animals sampled after two durations of steady-state torpor, during two stages of spontaneous arousal episodes, and in animals after they ended hibernation. Significant seasonal and torpor-arousal cycle differences of gene expression were detected in genes involved in glycolysis, fatty acid metabolism, gluconeogenesis, amino acid metabolism, molecular transport, detoxification, cardiac contractility, circadian rhythm, cell growth and apoptosis, muscle dystrophy, and RNA and protein protection. We observed, for the first time, complex modulation of gene expression during multiple stages of torpor-arousal cycles. The mRNA levels of certain metabolic genes drop significantly during the transition from late torpor to early arousal, perhaps due to the rapid turnover of mRNA transcripts resulting from the translational demands during thermogenesis in early arousal, whereas the mRNA levels of genes related to circadian rhythm, cell growth, and apoptosis rise significantly in the early or late arousal phases during torpor-arousal cycle, suggesting the resumption of circadian rhythm and cell cycle during arousal.