The study aimed at assessing stunting and wasting as correlates of body composition in Cambodian children. As part of a nutrition trial (ISRCTN19918531), fat (FM) and fat-free mass (FFM) were measured using 2H dilution at 6 and 15 months of age. Linear mixed-effects models were used to assess associations of stunting, wasting, sex and breastfeeding with FM and FFM and height-adjusted indexes FMI and FFMI. Of 419 infants enrolled, 98% were breastfed, 15% stunted and 4% wasted at 6 months. At 15 months, 78% were breastfed, 24% stunted and 11% wasted. Those not breastfed had lower FMI at 6 months (-1.22; 95% CI -2.05;-0.39) but not at 15 months (-0.23, -0.51;0.051). Stunted children had lower FM at 6 months and lower FFM at 6 and 15 months compared to children with length-for-age ≥0 Z. Stunting was not associated with FMI or FFMI. Wasted children had lower FM, FFM, FMI and FFMI at 6 and 15 months compared to children with weight-for-length z (WLZ) ≥0. Generally, FFM and FFMI deficits increased with age, whereas FM and FMI deficits decreased, reflecting interactions between age and WLZ. For example, the FFM deficits were -0.99 (-1.26;-0.72) kg at 6 months, and -1.44 (-1.69; -1.19) kg at 15 months (interaction, p<0.05), while the FMI deficits were -2.12 (-2.53;-1.72) kg/m2 at 6 months and -1.32 (-1.77;-0.87) kg/m2 at 15 months (interaction, P<0.05). This indicates that undernourished children preserve body fat at the detriment of fat-free tissue, which may have long-term consequences for health and working capacity.