It is not clear what dietary intake standards should be used for children with abnormal body size. To investigate the energy requirements of short-stature children with no underlying diseases, their resting energy requirements (REE) were measured by indirect calorimetry. The short-stature group consisted of 30 prepubertal children with short stature and with no underlying diseases (age 6y±2) and the control group consisted of 13 age-matched children with standard stature. Fasting REE and the respiration quotient (RQ) with subjects in the supine position were measured by canopy indirect calorimetry. Actual measurements and body-size-adjusted REEs were compared between the groups. Also, REE measurements were compared with the basal metabolic rate (BMR) calculated using the Dietary Reference Intakes for Japanese (Dietary Reference Intakes). REE in the control group was significantly higher than that in the short-stature group. However, body-size-adjusted REEs were significantly higher for the short-stature group. When the actual REE was compared with the calculated BMR within both the control group and the short-stature group, which was acquired using the Dietary Reference Intakes, there was no difference within the control group but the actual REE measurements were significantly higher than the calculated BMR in the short-stature group. The same pattern was seen within the short-stature group when subjects were matched for height. There were no significant differences in RQ between the two groups.