The objective of this cross-sectional study was to evaluate the relationship between micronutrient status and obesity, lipids, insulin resistance and chronic inflammation in children. Weight, height, waist circumference and body composition (dual-energy X-ray absorptiometry (DEXA)) were determined in 197 school-aged children. Lipids, glucose, insulin, C-reactive protein (CRP), zinc, iron and vitamins A, C and E were analyzed in blood. Vitamin C and vitamin E:lipids were negatively associated with Body Mass Index (BMI), waist-to-height ratio (WHR) and body and abdominal fat (p < 0.05). Vitamin A was positively associated with BMI, BMI-for-age, WHR and abdominal fat (p < 0.05). Iron and vitamin E:lipids were negatively associated with insulin (p < 0.05). Vitamins A, C and E and iron were negatively associated with CRP (p < 0.05). Interaction analysis showed that children who were overweight and obese who also had low concentrations of vitamin A had higher CRP and lower triglycerides (p < 0.1), children with low vitamin E had significantly lower glucose and triglycerides (p < 0.1) and higher low-density lipoprotein (LDL) concentrations (p < 0.05), and children with low zinc concentrations had higher insulin resistance compared with children with adequate weight (p < 0.05). In conclusion, low vitamin C concentration and vitamin E:lipids were associated with obesity. Furthermore, low concentrations of zinc, vitamins A and E in children who were overweight and obese were associated with lipids, inflammation and insulin resistance.