To investigate, at the molecular level, the remodeling of small intestine during amphibian metamorphosis, a subtractive hybridization approach was used to identify genes that are differentially regulated by thyroid hormone. A frog cDNA was isolated from Xenopus laevis and determined to be the gene encoding the intestinal fatty acid-binding protein (IFABP) based on its high sequence homology to the previously cloned mammalian IFABP gene. Northern blot analyses and in situ hybridization histochemistry also showed that, like the mammalian IFABP genes, frog IFABP gene expression is restricted to the intestinal epithelium. Xenopus embryos express detectable IFABP mRNA at stage 33/34, suggesting that intestinal epithelial cells differentiate well before feeding begins at stage 45. Moreover, during metamorphosis, levels of IFABP mRNA were gradually down-regulated over a period of about 20 days between stages 54 and 62, reaching a minimum at metamorphic climax, after which they were reelevated as the secondary epithelium forms. This reduction in IFABP gene expression could be reproduced in only 3 days by treating premetamorphic tadpoles with thyroid hormone. Our findings also show that this effect, while likely to be indirect, takes place before overt morphological changes are evident in primary epithelial cells. Thus, the down-regulation of IFABP mRNA is one of the early molecular events preceding epithelial cell death during intestinal remodeling.