Objective To investigate the correlation of variations of ABCB11 gene and primary intrahepatic stone (PIS).Methods The retrospective case-control study was conducted.The clinical data of 319 patients with PIS and 344 healthy controls who were admitted to the Southwest Hospital of the Third Military Medical University between December 2012 and December 2015 were collected.Three hundred and ninteen patients with PIS and 344 healthy controls were respectively allocated into the PIS and control groups.Twenty-seven exons in ABCB11 gene were detected via polymerase chain reaction (PCR) and DNA sanger sequencing.Observation indicators included:(1) variations and genotype frequency distribution of ABCB11 gene in the 2 groups;(2) correlation analysis between variations of ABCB11 gene and clinical data of patients with PIS:preoperative indicators of liver function test,recurrent episodes of cholangitis,preoperative obstructive jaundice,type and recurrence of stones.Comparison between groups in variations and genotype frequency distribution of ABCB11 gene was analyzed by the Logistic regression.The Kruskal-Wallis H test was performed to explore the correlation between genotype of ABCB11 gene and clinical test results of patients with PIS.Correlation between genotype of ABCB11 gene and clinicopathological data of patients with PIS was analyzed by the chi-square test.Results (1) Variations and genotype frequency distribution of ABCB11 gene in the 2 groups:whole-exome sequencing results showed that synonymous mutations of rs3815675,rs2287616 and rs497692 and missense mutations of rs2287617,rs2287622 and rs118109635 in the PIS group were respectively detected in exon 4,9,24 and 9,13,21.CT genotype frequency of rs118109635 was 4.70％(15/319) in the PIS group and 1.45％ (5/344) in the control group,respectively,with a statistically significant difference [OR=3.49,95％ confidence interval (CI):1.17-10.40,P＜0.05].GG and AG+GG genotype frequency of rs497692 were 46.08％ (147/319),87.46％ (279/319) in the PIS group and 37.79％ (130/344),79.36％ (273/344) in the control group,respectively,with a statistically significant difference (OR=1.73,1.65,95％ CI:1.05-2.83,1.04-2.61,P＜0.05).(2) Correlation analysis between variations of ABCB11 gene and clinical data of patients with PIS:levels of glutamyl-transpeptidase (GGT),alkaline phosphatase (ALP) and direct bilirubin (DBil) in the PIS group were 167 U/L (range,7-1 968 U/L),166 U/L (range,36-1 527 U/L),4 μmol/L(range,1-272 μmol/L) in the CC genotype of rs118109635 and 433 U/L(range,17-864 U/L),232 U/L (range,85-613 U/L),6 μmol/L(range,2-173 μmol/L) in the CT genotype of rs118109635,respectively,with a statistically significant difference (H=6.025,5.879,8.056,P＜0.05).Globulin level of PIS group was respectively 32 g/L (range,20-40 g/L),34 g/L(range,17-50 g/L) and 33 g/L(range,14-49 g/L) in the AA,AG and GG genotype of rs497692,respectively,with a statistically significant difference (H=12.119,P＜0.05).Of 81 patients with recurrence of PIS,GG and GA genotypes of rs2287617 were detected in 78 and 3 patients,respectively,with a statistically significant difference (x2=5.367,P＜0.05);TT,TC and CC genotypes of rs2287622 were detected in 12,39 and 30 patients,respectively,with a statistically significant difference (x2=6.153,P＜0.05).Of 127 patients with obstructive jaundice,116 and 11 patients had CC and CT genotypes of rs118109635,respectively,with a statistically significant difference (x2=7.381,P＜0.05);11,43 and 73 patients had AA,AG and GG genotypes of rs497692,respectively,with a statistically significant difference (x2 =11.364,P＜0.05).Conclusion There is a correlation between rs118109635 and rs497692 of ABCB11 gene and PIS,meanwhile,the above variation loci are associated with obstruction of biliary tract and cholestasis.