Infants with extrahepatic biliary atresia (EHBA) commonly develop rickets in infancy, whereas long-term survivors with EHBA commonly develop osteopenia with increasing age. We evaluated baseline vitamin D (D2and D3), 25-OH vitamin D2and D3, 1,25(OH)2vitamin D, bone mineral content, and vitamin D2and 25- OH vitamin D3absorption in six infants and children (age 4-22 mo) with EHBA whose portoenterostomy failed to produce bile flow (group 1) and five infants and children (age 10/12 to 8-4/12 y) with EHBA whose portoenterostomy repair led to good postoperative bile flow (group 2). Baseline serum vitamin D2and D3were undetectable in all subjects in group 1 despite supplements of 2500-5000 IU/ day, whereas all group 2 subjects given supplements (doses 400-5000 IU/d) had measurable levels. Baseline serum 25-OH vitamin D was less than 15 ng/mL in five of six (three with rickets) in group 1, whereas only one in group 2 had concentrations less than 15 ng/mL. A significantly blunted rise of vitamin D2above baseline and reduced area under the absorption curve after 1000 IU/kg vitamin D2were found in group 1 patients compared to group 2 (both p<0.01), and five pediatric controls (both/*<0.01). The peak change and area under the absorption curve for serum 25-OH vitamin D3from baseline after 10µg/kg 25-OH vitamin D3 were significantly reduced for group 1 (both at least p<0.05) and group 2 compared to controls (both p<0.05). Malabsorption of supplemental doses of vitamin D compromises their efficacy to prevent rickets in infants with EHBA with poor bile flow after portoenterostomy. Despite severe malabsorption of vitamin D, we suggest that oral 25-OH vitamin D may be absorbed sufficiently to prevent rickets.