Objective Infants with Prader-Willi syndrome (PWS) are hypotonic and underweight before the onset of childhood obesity. This study evaluates body composition in the PWS infant and its relationship to energy expenditure. Study design Sixteen infants and toddlers with PWS (mean age, 12.4 +/- 6 months; eight female subjects) underwent analysis of body composition with dual-energy x-ray absorptiometry and deuterium dilution, and energy expenditure with both doubly labeled water and indirect calorimetry. Results Percent body fat was significantly increased (male subjects, P < .001; female subjects, P < .001) and fat-free mass (FFM) was significantly decreased (male subjects, P < .001; female subjects, P =.04) in infants with PWS when compared with age-matched published data for normal infants. Meanwhile, total energy expenditure was significantly decreased (male subjects, P =.025; female subjects, P < .001) in infants with PWS when compared with published normative data. There was a normal relationship between FFM and total energy expenditure in infants with PWS. Conclusion Compared with published data for infants without PWS, infants with PWS demonstrate increased percent body fat, decreased FFM, and decreased energy expenditure. Importantly, total energy expenditure per kilogram of FFM appears similar in infants with and without PWS. We conclude that lower energy expenditure in infants with PWS is caused by decreased FFM.