Variations in genes encoding canalicular transportes, for biliary lipids may affect concentrations of biliary lipids in bile and promote cholesterol crystallization and gallstone formation. In our study we investigated the contribution of heterozygosity for common variations considered either potentially pathogenic or susceptibility alleles for cholesterol cholelithiasis in adults (c.523A>G (p.Thr175Ala) and c.1954A>G (p.Arg652Gly) in ABCB4, c.1331T>C (p.Val444Ala) in ABCB11 and c.55 G>C (p.Asp19His) in ABCG8) to the aetiology of paediatric idiopathic gallstone disease. Genotyping was performed in 35 paediatric subjects with idiopathic gallstones with positive family history for gallstones and 150 population controls. The ABCB4 variant p.Thr175Ala was found only in the controls, not in the patients. The frequency of the remaining three variant alleles and the corresponding genotypes did not differ between patients and controls. We conclude that the studied common variations in genes encoding canalicular transporters known to contribute to genetic predisposition to cholesterol gallstones in adulthood do not contribute specifically to the aetiology of paediatric idiopathic gallstones.