<b><i>Aim:</i></b> To assess bone health in pediatric intestinal failure (IF). <b><i>Methods:</i></b> A population-based cohort of 41 IF patients (age 9.9 years) underwent evaluation of bone mineral density (BMD), bone biochemistry, nutritional status and growth. Eleven patients remained on parenteral nutrition (PN) after 69 months. Thirty had weaned off PN 9.0 years earlier (mean), i.e. after 30 months on PN. <b><i>Results:</i></b> The majority of patients had lumbar spine or femoral BMD Z-score ≤-1.0 (70%), vitamin D deficiency (serum 25-hydroxyvitamin-D, S-25-OHD, <50 nmol/l, 41%) or secondary hyperparathyroidism (plasma parathyroid hormone >47 ng/l, 44%), equally during and after weaning off PN. Hyperparathyroidism was absent when S-25-OHD was >80 nmol/l. Until puberty, height (-1.4 to -0.8, age 1-12) and weight Z-scores (-1.3 to -0.5, age 1-16) were below the normal mean (p < 0.05). Small bowel length associated with S-25-OHD levels (r = 0.489, p = 0.013). In a multivariate model, time after weaning off PN (β = -0.597, p = 0.001), duration of PN (β = -0.466, p = 0.006) and calcium intake (β = -0.331, p = 0.035) predicted decreased lumbar spine BMD. <b><i>Conclusions:</i></b> In pediatric IF, vitamin D insufficiency, secondary hyperparathyroidism and decreased BMD are common. BMD, vitamin D, calcium and nutritional status should be closely monitored during and after weaning off PN to ensure sufficient vitamin D and mineral substitution for normal growth and bone mass attainment.