The enteric nervous system (ENS) can control most essential gut functions owing to its organization into complete neural circuits consisting of a multitude of different neuronal subtypes. We used microarrays to identify transcription factor networks and signaling pathways involved in diversification and differentiation of enteric neurons during development of the enteric nervous system. Overall design: In total four enteric samples and two non-ENS bowel samples were isolated (3-4 replicates of each) by FACS sorting of bowel cells from transgenic mouse reporter lines. Progenitor ENS cells (which express Sox10) were isolated from Sox10CreERT2 x R26ReYFP bowel at E11.5 (S11plus-S14plus) and E15.5 (S51plus-S54plus), 20 hours after YFP-reporter had been induced with 4-OHT. Whole ENS populations were isolated from Wnt1Cre x R26ReYFP bowel at E11.5 (W11plus-W13plus) and E15.5 (W51plus-W53plus). Negative populations in the FACS sorting of Wnt1Cre x R26ReYFP were harvested as non-ENS bowel cells at E11.5 (W11minus-W13minus) and E15.5 (W51minus-W53minus). Total RNA from each sample was converted to cDNA and hybridized on Affymetrix microarrays.