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Background  The prevalence of obesity and associated risk of chronic diseases are increasing among the paediatric population. The effectiveness of preventive measures and interventions are likely to improve when all factors which associate with obesity in a specific target group are considered. Currently such comprehensive data is unavailable for Sri Lankan children aged 8–9 years.    Methods  This paper pertains to the data collected from August-2015 to November-2016 for a case-control study which included cases (high body fat) ( N  = 160; males-81) and controls (normal body fat) ( N  = 164; males-80) recruited from primary schools in the Colombo Municipal area. Anthropometry and body composition (Bioelectrical impedance analysis-BIA) were measured. Diet, physical activity and socio-demographic data were collected using validated interviewer administered questionnaires. Serum concentrations of vitamins A, D [25(OH)D], E, folate (serum and red blood cell-RBC), zinc (Zn), selenium (Se), copper (Cu), iron (Fe), magnesium (Mg), calcium (Ca), chromium (Cr), manganese (Mn), cobalt (Co), ferritin, leptin and high sensitivity C-reactive protein (hs-CRP) were assessed using fasting blood samples.    Results  Cases were from higher socio-economic strata and spent significantly less time on physical activities, more time on sedentary behaviours and consumed higher energy compared to the controls. Cases from both genders had significantly lower levels of vitamin D [25 (OH)D], Fe and Mg ( all p  < 0.05) and higher levels of Cu and Ca ( all p  < 0.01) compared to controls. Higher levels of ferritin and Cr were seen among male ( p  < 0.001) and female ( p  > 0.05) cases compared to the controls. However, total serum folate levels were lower in male ( p  < 0.01) and female ( p  > 0.05) cases while the RBC folate levels were higher among male ( p  < 0.01) and female ( p  > 0.05) cases compared with controls. Vitamins A, E, Se, Mn and Co ( p  > 0.05) were not significantly different between groups. The inflammatory markers, both hs-CRP and leptin levels were higher among cases ( p  < 0.001) compared to the controls.    Conclusions  This study highlights higher socio-economic status, lower physical activity, more sedentary behaviours, higher energy intake and inconsistent distribution of micronutrients among the children with high body fat when compared with the control group. Increased levels of inflammatory markers indicate the presence of the risk of chronic inflammation in children with high body fat.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12887-020-02473-3.

Micronutrient status and associated factors of adiposity in primary school children with normal and high body fat in Colombo municipal area, Sri Lanka