BACKGROUND: The role of microbiota in biliary atresia (BA) remains unclear. The aim of our study was to assess efficacy and safety of LGG treatment in children with BA after HPE with special focus on bacterial cholangitis (BCH) and quantitative assessment of the gut microbiota composition and metabolism. METHODS: We performed double-blind placebo controlled trial with patients randomized into treatment group who received LGG (n = 14) and placebo (n = 16). The gut microbiota and short-chain fatty acids (SCFA) were assessed at baseline and after 6 months of treatment. Clinical and laboratory parameters including episodes of bacterial cholangitis (BCH) were collected during the study period and after 2-year follow-up. Additionally, stool composition of BA patients was compared with healthy age-matched control group. RESULTS: There were lower concentration of SCFA in children with BA compared to control group and significant increase in the number of Enterococcus bacteria. After 6 months of treatment, neither laboratory parameters nor gut microbiota composition differed between LGG group and placebo. PP analysis results were similar to ITT analysis, no significant differences between study and control group. Overall, there were 11 (36%) patients who developed at least one episode of bacterial cholangitis; 3 (21%) in the LGG group compared to 8 (50%) placebo group (p = 0.14). Bacterial cultures were positive in 22% of cases and recurrence after the first episode was observed in 27% of patients. The level of total bilirubin decreased below 2 mg/dl after 6 months of the study in 6 (42.8%) patients in the LGG group and in 8 (50%) patients in the placebo group (p = 0.73). During 2-year follow-up 6 out of 14 patients (42.8%) in the LGG group and 11 out of 16 placebo patients (68.7%) underwent liver transplantation (p = 0.27). CONCLUSIONS: Patients with BA present with specific microbiota profiles and decreased SCFA what gives opportunities to implement novel therapeutic options based on modulation of  microbiota. Whether LGG is an effective therapy needs to be studied in a larger group with similar outcome parameters.