Genes induced by thyroid hormone (TH) to change their expression in the Xenopus laevis gastrointestinal (GI) tract have been isolated using a subtractive hybridization method. An exhaustive search for down-regulated genes identified a single gene. Thirty-two different cDNA fragments derived from the up-regulated mRNA of tadpole intestine 18 h after addition of TH were cloned. They map to no more than 22 distinct genes. The isolation of multiple cDNA fragments derived from a single mRNA indicates that the complexity of up-regulated genes is limited. Both ubiquitous and intestine-specific up-regulated genes were found in this screen. The majority of these genes respond directly to TH induction as judged by the resistance of up-regulation to inhibitors of protein synthesis. The biological significance of these genes is supported by their dramatic regulation in the GI tract during spontaneous metamorphosis.