Abstract Background and aims Several studies demonstrated that larger neck circumference (NC) in children and adolescents may help to identify obesity and cardio-metabolic abnormalities. We aimed to evaluate the correlation between NC and metabolic syndrome (MetS) risk factors and to determine the utility of this anthropometric index to identify MetS in European children. Methods and results The present cross-sectional analysis includes 15,673 children (3–10 years) participating in the IDEFICS study. A continuous MetS (cMetS) score was calculated summing age and sex standardized z -scores of specific MetS risk factors. Receiver Operating Characteristic analysis, stratified by one-year age groups, was used to determine the ability of NC to identify children with unfavorable metabolic profile, corresponding to cMetS score ≥ 90th percentile. The areas under the curve values for NC associated with cMetS score values ≥ 90th percentile were significantly greater in girls than in boys ( p  < 0.001), except for 5 < 6 years group. For boys, optimal NC cut-off values ranged from 26.2 cm for the lowest age group (3 < 4 years), up to 30.9 cm for the highest age group (9 < 10 years). In girls, corresponding values varied from 24.9 cm to 29.6 cm. Conclusion The study demonstrated the efficacy of NC in identifying European children with an unfavorable metabolic profile.