Growth failure and malnutrition are common clinical features in cystic fibrosis (CF), but the relationships among resting energy expenditure (REE), pulmonary function, and nutritional status, are poorly understood. To better understand these relationships, REE, growth, nutritional status, and pulmonary function were measured prospectively in 25 prepubertal children with CF and 26 prepubertal control subjects of similar age and gender over a 3-y period. All subjects with CF had pancreatic insufficiency and mild pulmonary disease. REE was elevated for the CF children compared with control subjects throughout the study. This increased REE was not associated with declining pulmonary function. Longitudinal analyses revealed different patterns of change over time in boys and girls, such that REE significantly increased in the girls with CF and pulmonary function decreased in the boys. Boys with CF experienced a decline in weight Z score and percent ideal body weight, whereas the girls with CF experienced a decline in height Z score. Pulmonary function was not associated with REE, but nutritional status (percent ideal body weight) and genotype (delta F508 homozygotes versus others) were predictive of changes in pulmonary function over time. Fat free mass and height were found to be the best predictors of REE, and after accounting for these important body size and composition variables, differences in REE between boys and girls and CF and control groups increased over time. These findings identify the importance of investigating gender differences in the course of disease and considering REE as an early indicator of disease severity independent of pulmonary function.