AIM: To evaluate microbial colonization of upper aerodigestive tract in children and to investigate the influence of adenoid hypertrophy, allergy and exposition to cigarette smoke on presence of pathogens. METHODS: In 43 children with adenoid hypertrophy and 17 healthy children bacterial culture was performed by a swab from middle nasal meatus, nasopharynx and tonsils. The effect of adenotomy, presence of allergy and exposure to passive smoking on bacterial colonization were investigated. RESULTS: Identification of potentially pathogenic bacteria in upper aerodigestive tract was significantly higher in children with adenoid hypertrophy compare to control group. Adenotomy was associated with significantly decreased colonization by potential pathogens. Allergy was diagnosed in 33 % children with adenoid hypertrophy. Presence of allergy and exposure to tobacco smoke were associated with significantly more often colonization by potentially pathogenic bacteria in the upper aerodigestive tract. CONCLUSION: Increased colonization of upper aerodigestive tract by potential pathogens and their significant decrease after adenotomy indicate the role of pathogenic bacteria in the etiopathogenesis of adenoid hypertrophy. Allergy and tobacco smoke exposure are related to increased colonization by potentially pathogenic bacteria in the upper aerodigestive tract.