Colonization of middle ear pathogens (S. pneumoniae, H. influenzae and B. catarrhalis) in the nasopharyngeal opening of the Eustachian tube (NO) was charted in 94 patients (170 ears) suffering from secretory otitis media (SOM). Subsequent determination of microorganisms in the middle ear effusion was performed. 76% of the patients had colonization of pathogens in the NO, while pathogens colonized the middle ear cavity (MEC) in 30% of the cases. Predominant pathogen was S. pneumoniae, followed by B. catarrhalis and H. influenzae. When colonizing the MEC, there was a 100% correlation to NO regarding B. catarrhalis, 81% correlation for S. pneumoniae and 57% for H. influenzae. S. aureus and/or coagulase-negative staphylococci were only occasionally found in the NO. Accumulation of a sticky glue effusion material in the middle ear cavity may serve as a barrier against ascending pathogens from the nasopharynx.