Small heterodimer partner (SHP) is an orphan nuclear receptor which gene expression can be up-regulated by bile acids. It regulates its target genes by repressing the transcriptional activities of other nuclear receptors including NeuroD, which has been shown to regulate secretin gene expression. Here, we evaluated the regulation on duodenal secretin gene expression by SHP and selected bile acids (cholic acid (CA) and chenodeoxycholic acid (CDCA)). In vitro treatment of CDCA or fexaramine elevated SHP transcript level and occupancy on secretin promoter. The increase in SHP level, induced by bile acid treatment or overexpression, reduced secretin gene expression, while this gene inhibitory effect was reversed by silencing of endogenous SHP. In in vivo studies, double-immunofluorescence staining demonstrated the coexpression of secretin and SHP in mouse duodenum. Feeding mice with 1% CA-enriched rodent chow resulted in up-regulation of SHP and a concomitant decrease in secretin transcript and protein levels in duodenum comparing to control group fed with normal chow. 5% cholestyramine (CY)-enriched diet led to a decrease in SHP level and a corresponding increase in secretin expression. Overall, this study showed that bile acids via SHP inhibit duodenal secretin gene expression. As secretin is a key hormone that stimulates bile flow in cholangiocytes, this pathway thus provides a novel means to modulate secretin-stimulated choleresis in response to intraduodenal bile acids.