Parasitic helminth infections can suppress symptoms of allergy, type 1 diabetes, arthritis, and inflammatory bowel disease in animal models. We analyzed data from a large, population-based cohort study to determine whether common childhood enterobiasis protects against these diseases. We collected information on individual prescriptions filled for the drug Mebendazole against Enterobius vermicularis for all children born in Denmark 19952008 from the National Register of Medicinal Product Statistics (n = 924,749; age 014 years); 132,383 of these children (14%) filled a prescription for Mebendazole, 102,482 of the children (11%) had a household peer who was registered with a filled Mebendazole prescription, and the remaining 689,884 children (75%) comprised the reference group. Children diagnosed with asthma, type 1 diabetes, juvenile arthritis, ulcerative colitis, or Crohn's disease were identified from the National Patient Registry. We used Poisson regression to estimate confounder-adjusted incidence rate ratios for first in- or outpatient hospital diagnosis of chronic inflammatory disease according to history of Mebendazole treatment prescribed to children in the study. Chronic inflammatory disease was diagnosed in 10,352 children during 6.4 million person-years of follow-up. The incidence rate ratios was 1.07 for asthma (95% confidence interval [CI]: 1.001.13), 1.05 for type 1 diabetes (95% CI: 0.791.12), 1.13 for juvenile arthritis (95% CI: 0.941.37), 0.77 for ulcerative colitis (95% CI: 0.411.46), and 1.44 for Crohn's disease (95% CI: 0.822.53). Results were not modified by number of treatments or age at treatment. Based on a population-based analysis, enterobiasis does not reduce risk for asthma, type 1 diabetes, arthritis, or inflammatory bowel disease.