The aim of the present study was to evaluate associations between intestinal parasitic infection with intestinal and systemic inflammatory markers in school-aged children with high rates of obesity. Plasma concentrations of C-Reactive Protein (CRP), leptin, TNF-α, IL-6 and IL-10 were measured as systemic inflammation markers and count of stool leukocytes as marker of intestinal inflammation in 291 children (6-10 years). Intestinal parasitic infection was measured by stool examination. Logistic regression analyses were performed to determine the odds of having high inflammatory markers for each parasite or group of parasites as compared to parasite-free children while adjusting for sex, age, mother's educational level and percentage of body fat. The prevalence of soil-transmitted helminths and intestinal protozoa infections was 12% and 36%, respectively. Parasitic infection was not associated with CRP, IL-6, IL-10 or TNF-α. Children infected with Ascaris lumbricoides (aOR: 5.91, 95% CI: 1.97-17.70) and Entamoeba coli (aOR: 8.46, 95% CI: 2.85-25.14) were more likely to have higher stool leucocytes than parasite-free children. Children with multiple infections (aOR: 10.60, 95% CI: 2.85-25.14) were more likely to have higher leptin concentrations than parasite-free children. Intestinal parasitic infection was not associated with systemic inflammation, but was associated with intestinal inflammation. Having multiple infections were associated with higher leptin concentrations.