Air displacement plethysmography utilises a two-component model to assess body composition, which relies on assumptions regarding the density of fat-free mass (FFM). To date, there is no evidence as to whether Lohman’s or Wells et al.’s FFM density values are more accurate in young children. Therefore, the aims of this study were to compare total body fat percentage (TBF%) assessed using the BodPod with both Lohman’s and Wells et al.’s FFM density values with TBF% from the three-component (3C) model in forty healthy Swedish children aged 5·5 years. Average TBF% calculated using Lohman’s FFM density values underestimated TBF% in comparison with the corresponding value assessed using the 3C model (22·2 (sd 5·7) and 25·1 (sd 5·5) %, respectively; P<0·001). No statistically significant difference was observed between TBF% assessed using Wells et al.’s FFM density values and the 3C model (24·9 (sd 5·5) and 25·1 (sd 5·5) %, respectively; P=0·614). The Bland and Altman plots for TBF% using both Lohman’s and Wells et al.’s FFM density values did not show any bias across the range of body fatness (Lohman: r 0·056, P=0·733 and Wells et al.: r −0·006, P=0·970). These results indicate that Wells et al.’s FFM density values should be used when assessing body composition with the paediatric option for BodPod in 5-year-old children. However, future studies are needed to confirm these results in other populations, including a wider age range of children.