A healthy diet is crucial in childhood because it affects the physical and cognitive development of children. By promoting healthy eating habits, we also influence healthy nutrition choices later in life. The purpose of this study was to gain insight into children’s eating habits, school nutrition and its impact on the increased risk of developing of metabolic syndrome (ptMS). The survey began in the fall of 2017 and included 63 children of the final grade of five elementary schools across Slovenia and their parents. We further divided them by the type of school: ECO (participate in an international program of ECO schools) schools and others. The research included telephone survey of one of the parents and the child answering questions from a socio-demographic and a food frequency questionnaire. Anthropometric data were obtained from sport records and fat ratio was calculated subsequently. Boys and girls who attended ECO schools did not have significantly lower BMI (p=0,699 and p=0,789) and fat percentage (BFP) (p=0,920 and p=0,504) than those who attended other schools, but boys did have significantly lower BFP than girls (p=0,000). However, children in ECO schools consumed more vegetables (p=0,004), whereas the hypothesis of more fruit consumption (p=0,872) and less sugar consumption (p=0,076) was not confirmed. Regardless of the school type and gender, sugar intake on average represented 15% of daily energy intake. 70.0 % of children had breakfast daily, 87,3 % has at least four meals a day. After calculating tri-ponderal mass index (kilogram body weight/m3), we found that 60,3% of children were at risk of MS, more boys (60,5 %) than girls (39,5 %), although it has to be stressed that the methodology used differed from the originally published. Girls had statistically higher fat mass index (kilogram fat mass/ m3) than boys (p=0,030). We have not statistically demonstrated that school type has an effect on ptMS. For more accurate and realistic assessment of the impact of school nutrition on the occurrence of MS in Slovenian children, it would be necessary to conduct a clinical study with more participants and a larger number of primary schools involved.