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Childhood obesity is an increasing threat to the health of primary school students in Hong Kong. Obesity results from energy excess from food relative to energy expenditure through physical activity. In Hong Kong, a whole day primary schooling policy has been implemented since 1993 and today most primary school students have their lunch on campus and some also purchase snacks and drinks from school tuck shops or vending machines. The EatSmart School Accreditation Scheme (ESAS) aiming at combating childhood obesity was launched in 2009/2010. Professional (health promotion, dietary, programme, etc.) support is provided to help schools formulate policies, introduce structures and implement measures to help students develop the habit of healthy eating. The aim of this study is to investigate the change of childhood obesity (including overweight) rates over time among schools awarded with ESAS accreditation. Seven-year retrospective data on obesity status were obtained for the period 2007/2008-2013/2014 (number of students = 113,322, number of measurements = 314,746) from all 105 ESAS-accredited schools. Before schools were geared up for the accreditation scheme obesity rates were fairly stable (slope test p > 0.05) among their student population ranging from 23.2% to 21.9%, whereas the rates dropped significantly (slope test p < 0.05) from 21.9% to 19.3% after intervention. For ESAS-accredited schools, there was an average annual reduction of 0.49% point in obesity rate which was 0.18% point higher than that of 0.31% point among non-ESAS-accredited schools. These results show that schools achieving ESAS accreditation are associated with a bigger improvement in the student obesity problem.