BACKGROUND AND AIMS: The zebrafish Danio rerio is an excellent model system for mammalian gastrointestinal development. To identify differentially regulated genes important in gastrointestinal organogenesis, we profiled the transcriptome of the zebrafish developing gastrointestinal tract. METHODS: Embryos from a transgenic zebrafish line expressing GFP in the developing intestine, liver, and pancreas were dissociated at four developmental timepoints, their cells sorted based on GFP expression using fluorescence-activated cell sorting (FACS), and analyzed with microarrays. To improve our analysis, we annotated the Affymetrix Zebrafish GeneChip with human orthologs. RESULTS: Transcriptional profiling showed significant differences between GFP+ and GFP- cells. Upregulated genes and pathways were consistent with mammalian gastrointestinal development, such as HNF gene networks, and cancer. We implicate the PI-3 Kinase pathway and show that inhibition with LY294002 causes gastrointestinal defects in zebrafish. We identified novel genes, such as the microRNAs miR-217 and miR-122, the tight junction protein claudin c, the gene fam136a, and a zebrafish tetraspanin. Novel pathways include genes containing a putative transcription factor binding sequence, GGAANCGGAANY, and a nucleolar gene network. The zebrafish microarrays also identify a set of 32 genes that may mediate the effects of gain of chromosome arm 8q in human colon, liver, and pancreatic cancers. CONCLUSIONS: We successfully combine fluorescence-activated cell sorting and microarray profiling to follow organogenesis throughout development. These experiments identify novel genes and pathways that likely play a role in mammalian gastrointestinal development and are potential targets for therapeutic intervention in the management of gastrointestinal disease and cancer.