Background Dysfunction of the hepatic canalicular membrane transporters BSEP (Bile Salt Export Pump) and MDR3 (Multidrug Resistance Type 3) is a cause of hereditary intrahepatic cholestasis. The aim of this study was to investigate, whether genetic variation in BSEP and MDR3 also plays a role in other chronic and acute cholestatic conditions such as (1) primary biliary cirrhosis (PBC), primary sclerosing cholangitis (PSC) and (2) intrahepatic cholestasis of pregnancy (ICP). Methods Genetic variation in BSEP and MDR393 was analyzed in (1) 93 healthy Caucasians (CA), 76 PBC, 46 PSC and (2) 21 ICP patients of Caucasian origin. Sequencing spanned ~10000 basepairs including promoter and all exons with 50 to 300 bp of flanking intronic region. Results The CA-PBC-PSC-collective showed no differences with respect to the number and allele frequency of variants per group, haplotype distribution and linkage disequilibrium. In the ICP-collective three non-synonymous sites in codons for evolutionarily conserved amino acids were specific for ICP (BSEP: N591S; MDR3: S320F and G762E). Furthermore, four ICP-specific splicing mutations were detected in MDR3: intron 21: G(+1)A, intron 25: G(+5)C and C(-3)G and intron 26: T(+2)A. Conclusion BSEP and MDR3 variant segregation and haplotype structure does not support a role of BSEP and MDR3 genetic variation in the pathogenesis of PBC and PSC. On the other hand, findings point towards a pathogenic role of MDR3 genetic variability in ICP. Clinical Pharmacology & Therapeutics (2004) 75, P94–P94; doi: 10.1016/j.clpt.2003.11.358