Magnetic Resonance Imaging (MRI) is increasingly being used in children to quantify adipose tissue (AT) and skeletal muscle (SM) in vivo. It is unclear whether the every 5 cm whole body MRI protocol used in adults is appropriate when applied in children. Whole body MRI continuous 1 cm thick slices were acquired in 73, aged 5-17-year-old healthy children. Images were segmented into subcutaneous (SAT), visceral (VAT), intermuscular AT (IMAT), and SM. The percentage difference between volumes measured by the continuous protocol and volumes estimated with protocols of different between-slice intervals (i.e., interval = 2, 3, 4 and 5 cm) was larger with an increase in interval size, depot size, weight and body mass index percentile. For group comparisons, studies will require less than 5.4% more subjects if an every 5 cm protocol is used for equivalent power as the every 1 cm protocol. For individual subject comparisons, interval protocols can be used to reliably distinguish between subjects who differ in SM or SAT volume by 0.14 to 0.64 L (i.e., 1 to 5% of SM or SAT volume) or more, or in VAT or IMAT volume by 0.06 to 0.21 L (i.e., 10 to 30% of VAT or IMAT volume) or more. The every 5 cm image acquisition protocol can be considered as accurate as the contiguous protocol for group comparisons in children, as well as for comparison of SM and SAT among individual children. However, a smaller slice interval protocol would be more accurate for comparison of VAT or IMAT among individual children.