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Without consideration for the effects of fat mass, there could be an underestimation of cardiorespiratory fitness in children with obesity leading to a clinical diagnosis of deconditioning and resulting in unrealistic training goals and limitation of physical activities. The purpose of this study was to identify methods of quantifying cardiorespiratory fitness that were less influenced by fat mass.Fifty-three children, 27 with obesity (10.9 ± 1.0 yr) and 26 without obesity (11.0 ± 1.0 yr), volunteered for this study. Maximal oxygen uptake, an indicator of cardiorespiratory fitness, was referenced to lean body mass, body mass, and predicted body mass at the 50th and 85th body mass index percentiles.Children with obesity carried 18 kg more fat mass and 7 kg more lean body mass compared with children without obesity. Cardiorespiratory fitness based on lean body mass, body mass, and predicted body mass at the 85th percentile was lower in children with obesity compared with children without obesity (P < 0.001). Differences in cardiorespiratory fitness based on predicted body mass at the 50th percentile between children with and without obesity did not reach statistical significance (P = 0.84). Fat mass influenced cardiorespiratory fitness least when referenced to lean body mass or predicted body mass at the 50th percentile (R2 < 0.26) in contrast to when it was referenced to body mass or predicted body mass at the 85th percentile (R2 > 0.37).Quantifying cardiorespiratory fitness based on lean body mass or predicted body mass at the 50th percentile could be useful for estimating fitness levels in children with obesity.