Purpose of reviewThyroid hormones are key regulators of development and metabolism that modulate transcription via nuclear receptors. Although the molecular actions of thyroid hormones have been thoroughly studied, their pleiotropic effects are mediated by complex changes in expression of numerous, but still largely unknown, target genes. This review summarizes the recent advances in the characterization of target genes in different organs.Recent findingsNew patterns of gene expression regulation have been described in tissues with known physiological actions of thyroid hormone, that is brain, liver, skeletal and cardiac muscles, and brown and white adipose tissues. The studies have benefited from the numerous transgenic models with altered thyroid hormone receptor expression and the application of DNA microarray technology to mouse and human tissues.SummaryData on thyroid hormone‐mediated control of gene expression and on the roles of the different thyroid hormone receptor isoforms bring new clues to our understanding of the molecular mechanisms of thyroid hormone action in physiological situations and, most importantly, in diseases associated with alterations of the thyroid status.