Objectives Chronic diarrhoea resulting from primary idiopathic bile acid malabsorption (IBAM) is common, but its aetiology is largely unknown. We investigated possible mechanisms, first looking for common sequence variations in the cytoplasmic ileal bile acid-binding protein (IBABP, gene symbol FABP6), and secondly, determining the expression of ileal mucosal transcripts for the apical sodium-linked bile acid transporter (ASBT), IBABP, the putative basolateral transporters, OST alpha and OST beta and regulatory factors.Methods Genomic DNA was prepared from two cohorts of patients and two control groups; the promoter and exonic regions of FABP6 were sequenced. In intestinal biopsies, transcript expression was measured by quantitative real time-PCR, using ileum from 17 patients and 21 controls.Results Sequence variations were identified in FABP6, but overall frequencies were similar in patients and controls. Transcripts of ASBT and IBABP, but not OST alpha and OST beta were expressed at higher levels in ileum than duodenum. The transcription factors fa rnesoid-X-receptor (FXR) and liver-receptor-homologue (LRH-1) were also more abundant in ileum, as was fibroblast growth factor 19 (FGF19), unlike short heterodimer partner (SHP), c-Fos, or CDX2. No significant differences in mean or median values were found between the groups for any of these transcripts. However, findings on regression analysis suggested that these transporters differ in their regulation, particularly in the relationships of CDX2, LRH-1 and FXR with OST alpha.Conclusion Most cases of IBAM are unlikely to be caused by genetic variation in FABP6 or by major differences in transporter transcript expression. Our evidence indicates that other factors, such as regulation of expression of the basolateral bile acid transporter, should be considered as possible causes.