FHL2 is a LIM domain protein that is able to form various protein complexes and regulate gene transcription. Recent findings showed that FHL2 is a potential tumor suppressor gene that was down-regulated in hepatocellular carcinoma. In the present study, microarray profiling of gene expression was performed to identify the genes regulated by FHL2 in mouse livers. The differentially expressed genes were further analyzed by bioinformatics tools including DAVID, KEGG, and STRING. Our data illustrate that FHL2 affects genes involved in various functions including signal transduction, responses to external stimulus, cancer-related pathways, cardiovascular function and regulation of actin cytoskeleton. Moreover, a network of differentially expressed genes identified in this study and known FHL2-interacting proteins was constructed. Then, genes identified by bioinformatics tools and most functional relevant to FHL2 were selected for further validation. Finally, the differential expression of Ar, Id3, Inhbe, Alas1, Bcl6, Pparδ, Angptl4, and Erbb4 were confirmed by quantitative real-time PCR. In summary, we have established a database of genes that are potentially regulated by FHL2 and these genes should be future targets for the elucidation of functional roles of FHL2. J. Cell. Biochem. 115: 744–753, 2014. © 2013 Wiley Periodicals, Inc.