Poor physical fitness is associated with increased health-related risks in children. The association of nutritional status indicators and physical fitness in children residing in developing countries is not well characterised. We conducted a cross-sectional study among 1945 children of age 5–12 years in Bogotá, Colombia, to assess whether anthropometric and micronutrient status indicators were associated with performance in the shuttle run and standing long jump tests. Stunted children scored significantly lower in the run (0·4 s; P = 0·0002) and jump (6 cm; boys only; P = 0·003) tests than non-stunted children, after adjustment for age and other factors. Children who were thin, overweight or obese ran slower than normal-weight children (P < 0·01). Lower jump scores were associated with overweight or obesity and greater arm fat area in boys only (P < 0·0001). Girls with low ferritin concentrations ran 0·6 s slower than girls with normal ferritin concentrations (P = 0·02). Erythrocyte folate concentrations were linearly related to higher run (P < 0·0001) and long jump scores (P = 0·0001). Boys with marginal or low vitamin B12 status had 4 cm lower long jump scores than children with normal status (P = 0·01). Suboptimal anthropometric and micronutrient status are related to poorer performance in fitness tests. The effects of improving nutritional status on physical fitness of children warrant investigation.