OBJECTIVE: To study the nasopharyngeal colonization in otitis-prone children before and after adenoidectomy. METHODS: The study population consisted of 35 children between 11 months and 4 years of age, undergoing adenoidectomy and tube placement for recurrent acute otitis media. All these children were otitis prone (OP). During general anesthesia, bacteriologic samples were obtained from the nasopharynx and the middle ear fluid, if present. During the follow-up visit, a new nasopharyngeal culture was taken. The control population consisted of 35 children undergoing surgery for non-ear-nose-throat pathology. These children had no history of recurrent upper respiratory tract infections. RESULTS: Colonization of the nasopharynx with potential pathogens (Streptococcus pneumoniae, Moraxella catarrhalis, Haemophilus influenzae) occurred significantly more in the OP children than in the non-OP children. Adenoidectomy resulted in a substantial decrease of potential middle ear pathogens in the nasopharynx and an increase of normal commensal flora. In about half of the patients, middle ear fluid was still present at the time of tube placement; in most instances, H. influenzae was cultured. Typing with arbitrarily primed PCR indicated substantial genetic diversity among the H. influenzae isolates studied. CONCLUSIONS: Both cross-colonization (between sampling sites within the same patient and between siblings) and turnover appeared to be high.