Introduction: State and private subsidized schools usually have limited resources that may restrict the frequency and quality of physical activities offered in educational establishments. Objective: to compare the physical condition of schoolchildren between 6-14 years of age attending state, private subsidized and private schools in the boroughs of the Metropolitan Region of Santiago. Methods: we worked with a random sample by sex and age of 1656 schoolchildren aged 6-14 years. Anthropometry was measured (weight, height, arm circumference, waist circumference and skin folds). In addition, horizontal jump without impulse, grip strength and the distance covered in the six-minute walk test were measured. Results: there was a significantly higher proportion of obesity and waist circumference above the 90th percentile observed in students from state schools, compared to their peers from private and subsidized private schools. At the same time, girls in state schools had significantly lower physical performance, particularly in tests of grip strength and horizontal jump (p < 0.01). Conclusion: State and subsidized schools tend to face resource limitations that may restrict the frequency and quality of physical activities offered. This may lead to lower results in physical fitness tests and, therefore, to a higher prevalence of risk indicators for cardiovascular and metabolic diseases in these students. Therefore, it is urgent to increase the quantity and quality of daily exercise time and to stimulate participation in sports to prevent and promote cardiovascular health.