NOX1, a member of the NOX family of NADPH oxidases, is expressed primarily in colon epithelium, where it may function in host defense and growth regulation. We investigated factors responsible for its transcriptional regulation in vitro and its expression in vivo. Analysis of promoter constructs in the CaCo2 cell line identified a complex element between -422 and -291 critical for promoter activity. This element contained four sites that bound GATA-4, -5, and -6 in vitro with varied affinities. One site also bound the caudal-related homeodomain proteins Cdx1 and Cdx2, whereas another also bound hepatocyte nuclear factor-1alpha (HNF-1alpha). GATA-6, HNF-1alpha, and Cdx2 also bound to this region in the intact chromatin of CaCo2 cells. These factors demonstrated cooperativity when transactivating the NOX1 promoter. NOX1 mRNA was detected in human colon epithelial cells along the crypt-villus axis. A gradient of NOX1 mRNA expression was seen in the colons of normal as well as germ-free mice, with significantly higher levels in distal compared with proximal segments. The expression gradients of NOX1 mRNA in the colon paralleled those of GATA-6, HNF-1alpha, and Cdx1. These data indicate that developmental, tissue-restricted transcription factors play a key role in NOX1 regulation in vivo.