Background: Previous studies suggest normal mineral status in children receiving elemental formula. However, a recent multicenter survey described 51 children who developed hypophosphatemia and bone disease while receiving elemental formula. Our aim is to determine the prevalence of metabolic bone disease in children receiving extensively hydrolyzed or amino acid-based formula. Methods: We established a retrospective cohort using an institutional database of tube-fed children. We defined a “confirmed case” as a child with biochemical and radiographic evidence of bone disease (rickets and/or low-trauma fractures). We defined a “suspected case” as a child who had biochemical evidence and/or radiographic evidence of bone disease but with incomplete data during the review period. Results: A total of 102 tube-fed children receiving elemental or semi-elemental formula were identified. The four elemental and semi-elemental formulas evaluated were Neocate®, EleCare®, Pregestimil®, and Alimentum®. Not all children had complete monitoring data performed during the review period. Of the children receiving Neocate who had monitoring data (46%), 23% developed hypophosphatemia and radiographic abnormalities (fractures or rickets), which resolved with phosphorus supplementation and/or change in the formula brand. Conclusions: We estimate that at least 11% and up to 23% of all tube-fed children receiving Neocate develop metabolic bone disease. Based upon the estimated prevalence, we recommend cautious use of this formula with monitoring for evolving bone disease in this population.