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The aim of the study was to evaluate health-related quality of life (HRQoL) and parental distress in a national cohort of children with biliary atresia (BA) with their native livers in relation to BA complications and HRQoL of normal population controls.We invited all Finnish children with BA surviving with their native livers at age 2 to 18 years to participate in 2009 and in 2014. Parents filled the Pediatric Quality of Life Inventory (PedsQL) proxy questionnaire, a survey of their child's health and evaluated parental distress on a visual-analog scale from 0 to 7. Overall participation rates were 80% (12/15) for the longitudinal and 83% (20/24) for the cross-sectional assessment. A control population of 324 children matched for age and sex was randomly picked, and 108 (33%) participated.Overall, patients and controls had comparable HRQoL. Patients reported significantly lower scores for school functioning (P = 0.004) as depicted by missing school or day care due to hospital visits. Eighty-five percent of parents reported extreme worry (7.0) when hearing their child's BA diagnosis. At 6 years after diagnosis, parents reported significantly less worry: median score 3.8 (interquartile range 3.0–5.4, P < 0.001 for difference). Parents of patients with optimal health were less worried than parents whose children's health was suboptimal: median worry score 3.3 (3.0–4.8) versus 5.3 (3.8–5.9), P = 0.05.BA patients’ HRQoL was comparable to matched peers in general but reduced by missing school days due to frequent hospital visits. At diagnosis, parents experienced considerable worry that diminished over the years after successful portoenterostomy, especially if the child's health was optimal.