A high-fat diet (HFD) leads to an increased risk of osteoporosis-related fractures, but the molecular mechanisms for its effects on bone metabolism have rarely been addressed. The present study investigated the possible molecular mechanisms for the dyslipidemic HFD-induced bone loss through comparing femoral gene expression profiles in HFD-fed mice versus the normal diet-fed mice during the growth stage. We used Affymetrix 430A Gene Chips to identify the significant changes in expression of the genes involved in bone metabolism, lipid metabolism, and the related signal transduction pathways. Quantitative RT-PCR was carried out on some significant genes for corroboration of the microarray results. At the conclusion of the 12-week feeding, the down-regulation of most of the genes related to bone formation and the up-regulation of most of the genes related to bone resorption were observed in the HFD-fed mice, consistent with the changes in plasma bone metabolic biomarkers. Together, the HFD induced a decrease in the majority of the adipogenesis-, lipid biosynthesis-, and fatty acid oxidation-related gene expression, such as PPARg and APOE. Furthermore, some genes engaged in the related signal transduction pathway were strongly regulated at the transcript level, including IGFBP4, TGFbR1, IL-17a, IL-4, and P53. These results indicate that an HFD may induce inhibitory bone formation and enhanced bone resorption, thus causing adverse bone status.