Background/aim: We investigated the role of body flora and chronic inflammatory infections in the etiology of allergic disorders in Turkish children. Materials and methods: Forty pediatric asthma patients with positive skin prick tests and 40 age-matched healthy subjects with negative skin prick tests were enrolled in this cross-sectional study. Serum H. pylori IgG, viral hepatitis serology, IL-10, and TGF-beta levels were measured. Stool and throat cultures were taken and tested for occurrence of microorganisms. Results: A significantly higher percentage of nonatopic subjects tested positive for anti-H. pylori antibodies compared to atopic subjects (60% vs. 20%). Serum IL-10 levels were also significantly higher in nonatopic subjects. No significant differences in direct microscopy and culture specimens of stools were observed. Examination of throat flora showed significantly higher occurrences of Neisseria and beta-hemolytic Streptococcus in nonatopic subjects, but higher occurrences of gram-positive bacilli in atopic subjects. Conclusion: Higher prevalence of anti-H. pylori antibody and higher serum levels of IL-10 in nonatopic subjects suggest that chronic infection and inflammation may protect against atopic disease. Higher occurrences of Neisseria and beta-hemolytic Streptococcus in throat cultures from nonatopic subjects are novel findings that lend further support to the hygiene hypothesis.