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The aim of this study was to assess associations between habitual school-day breakfast consumption, body mass index (BMI), physical activity (PA) and cardiorespiratory fitness (CRF).BMI, PA and CRF were measured in 4326 schoolchildren aged 10–16 years. Participants were classified as obese or non-obese, as having low or high PA and CRF. Habitual school-day breakfast consumption was assessed by a questionnaire and classified as never, sometimes or always.Participants who sometimes ate breakfast were more likely to be obese than those who always did (P<0.05). Boys who never ate breakfast were more likely to have low PA odds ratio (OR) 2.17, 95% CI 1.48–3.18) and low CRF (OR 2.02, 95% CI 1.40–2.93) than those who always did. Compared with those who always did so, girls were more likely to have low PA if they sometimes (OR 1.39, 95% CI 1.13–1.70) or never (1.48 95% CI 1.06–2.05) ate breakfast, but the likelihood of low CRF was not different between groups.Habitual breakfast consumption is associated with healthy BMI and higher PA levels in schoolchildren. In boys, regularly eating breakfast is also associated with higher levels of CRF. The higher PA observed in habitual breakfast eaters may explain the higher CRF values observed. These positive health behaviours and outcomes support the encouragement of regular breakfast eating in this age group.