Objective To study the function of Fkbp51 in the heart and liver by analyzing the differential RNA expression profiles in the wild-type mice (WT) and Fkbp51 knockout (KO) mice, and to elucidate the role of Fkbp51 gene in metabolic pathways in the heart and liver. Methods Using the second generation of high-throughput gene sequencing technology, the mRNA expression profiles of heart and liver were sequenced in WT and Fkbp51 KO mice. The data of sequencing of heart tissues were analyzed by DEGseq, and the results of sequencing of liver tissues were analyzed by BRB-Array Tools. The differential genes of the heart and liver in the mice were screened respectively. Gene ontology (GO) analysis and KEGG pathway analysis were performed to analyze the differentially expressed genes using the online tool DAVID. In addition, the differential genes of the two organ tissues were analyzed by Venn diagram. The interaction network of proteins was analyzed using the STRING database. Results (1) The absence of Fkbp51 led to changes in mRNA expressions of heart-related signal pathways such as vascular smooth muscle contraction, chemokine, retinol, and MAPK signaling pathways. (2) The lack of Fkbp51 mostly induced changes in cholesterol synthesis and metabolism, lipid metabolism, redox and other related genes and pathways in the liver. (3) In the heart and liver, Fkbp51 deletionresult ed in four co-differential genes, among them, down-regulation of Rnaset2b, Hmga1 and Fkbp51, while Cyp2b10 was down-regulated in the heart but up-regulated in the liver. All these proteins may interact with HSP90 protein and participat in the metabolism of heart and liver tissues. Conclusions Fkbp51 is involved in different metabolic and gene expression regulation pathways of heart and liver, and the roles are both independent and interrelated.