Localized neurological diseases such as spina bifida are often accompanied by normal upper limb and spinal bone mineral density (BMD), whereas regional BMD of the lower limbs may be decreased. Therefore, regional BMD measurements may be more accurate to quantify regional bone health. Until now, no pediatric reference centiles of bone mineral density and body composition of the lower extremities are available for Hologic DXA systems. The objective was to generate age-and sex specific reference centiles of DXA scans of lower limbs for Hologic DXA systems. Data from the National Health and Nutrition Examination Survey of the period 1999-2004 (age 8 - 20 years) were used to generate age-specific and sex-specific reference centiles for the non-Hispanic Black, non-Hispanic White and Mexican-American NHANES study population. The LMS method was used to calculate the reference centiles. Data of DXA scans of 2233 non-Hispanic black children (880 females), 1869 non-Hispanic white children (803 females) and 2350 Mexican American children (925 females) were used to create age-specific and sex-specific reference curves. We presented age-and sex-specific reference centiles for regional bone mineral density, bone mineral content, lean body mass and fat mass at the lower limbs for children and adolescents which were ethnicity specific and directly applicable to Hologic QDR-4500A fan-beam densitometer.