ABSTRACTObjectives:To describe bone status in children with Alagille syndrome (AGS) and healthy control children adjusted for age, gender and height (HT), and to identify dietary intake and AGS‐related factors associated with bone status.Methods:Prepubertal children with AGS and healthy controls comparable in age and ethnicity were evaluated. Subjects were ≥4 years of age, prepubertal and had whole body (WB) and/or lumbar spine (LS) dual energy X‐ray absorptiometry (DXA) scans of acceptable quality. Anthropometric (weight, HT), diet and AGS‐specific data (e.g., coefficient of fat absorption, labs, liver transplantation) were also collected. Bone area (BA), bone mineral content (BMC) and HT were log transformed for best fit. Bone data were analyzed unadjusted, adjusted for gender, age and HT, and as HT‐specific z‐scores.Results:AGS and control groups were similar in age, pubertal status and ethnicity. Children with AGS were small‐for‐age, had decreased BA and BMC‐for‐age, and decreased WB BA and BMC‐for‐HT z‐scores compared to healthy controls. Prevalence of low BMC‐for‐HT z‐scores (< −2) among AGS subjects was 20% for the WB and 39% for the LS. Bone mineralization was positively related to fat absorption but not dietary intake.Conclusions:Children with AGS have deficits in bone size and bone mass relative to body size. Modifiable factors, such as treatment of malabsorption should be explored as an early focus of AGS care to prevent bone fragility.