Little is known about the overall patterns of thyroid hormone (Th)‐mediated gene regulation by the main Th receptor (Tr) isoforms, Tr‐α and Tr‐β, in vivo. We used 48 complementary DNA microarrays to examine hepatic gene expression profiles of wild‐type and Thra and Thrb knockout mice under different Th conditions: no treatment, treatment with 3,3′,5‐triiodothyronine (T₃), Th‐deprivation using propylthiouracil (PTU), and treatment with a combination of PTU and T₃. Hierarchical clustering analyses showed that positively regulated genes fit into three main expression patterns. In addition, only a subpopulation of target genes repressed basal transcription in the absence of ligand. Interestingly, Thra and Thrb knockout mice showed similar gene expression patterns to wild‐type mice, suggesting that these isoforms co‐regulate most hepatic target genes. Differences in the gene expression patterns of Thra/Thrb double‐knockout mice and Th‐deprived wild‐type mice show that absence of receptor and of hormone can have different effects. This large‐scale study of hormonal regulation reveals the functions of Th and of Tr isoforms in the regulation of gene expression patterns.