Body composition assessment during infancy is important because it is a critical period for obesity risk development, thus valid tools are needed to accurately, precisely, and quickly determine both fat and fat-free mass. The purpose of this study was to compare body composition estimates using dual-energy x-ray absorptiometry (DXA) and air displacement plethysmography (ADP) at 6 months old. We assessed the agreement between whole body composition using DXA and ADP in 84 full-term average-for-gestational-age boys and girls using DXA (Lunar iDXA v11-30.062; Infant whole body analysis enCore 2007 software, GE, Fairfield, CT) and ADP (Infant Body Composition System v3.1.0, COSMED USA, Concord, CA). Although the correlations between DXA and ADP for %fat (r = 0.925), absolute fat mass (r = 0.969), and absolute fat-free mass (r = 0.945) were all significant, body composition estimates by DXA were greater for both %fat (31.1 ± 3.6% vs. 26.7 ± 4.7%; P < 0.001) and absolute fat mass (2,284 ± 449 vs. 1,921 ± 492 g; P < 0.001), and lower for fat-free mass (5,022 ± 532 vs. 5,188 ± 508 g; P < 0.001) vs. ADP. Inter-method differences in %fat decreased with increasing adiposity and differences in fat-free mass decreased with increasing infant age. Estimates of body composition determined by DXA and ADP at 6 months of age were highly correlated, but did differ significantly. Additional work is required to identify the technical basis for these rather large inter-method differences in infant body composition.