The prevalence of obesity continues to increase in the developing world. The effects of obesity on the cardiovascular system include changes in systolic and diastolic function. More recently obesity has been linked with impairment of longitudinal myocardial deformation properties in children. We sought to determine the effect of increased body mass index (BMI) on cardiac deformation in a group of children taking part in the population-based Southampton Women’s Survey to detect early cardiovascular changes associated with increasing BMI before established obesity. Sixty-eight children at a mean age of 9.4 years old underwent assessment of longitudinal myocardial deformation in the basal septal segment of the left ventricle (LV) using two-dimensional speckle tracking echocardiography. Parameters of afterload and preload, which may influence deformation, were determined from cardiac magnetic resonance imaging. BMI was determined from the child’s height and weight at the time of echocardiogram. Greater pediatric BMI was associated with greater longitudinal myocardial deformation or strain in the basal septal segment of the LV (β = 1.6, p < 0.001); however, this was not related to contractility or strain rate in this part of the heart (β = 0.001, p = 0.92). The end-diastolic volume of the LV increased with increasing BMI (β = 3.93, p < 0.01). In young children, regional deformation in the LV increases with increasing BMI, whilst normal contractility is maintained. This effect may be explained by the increased preload of the LV associated with increased somatic growth. The long-term implications of this altered physiology need to be followed-up.