Anaerobes contribute to the severity and chronicity of infections that occur in and around the oral cavity. One of the factors involved in the pathogenesis of otitis media with effusion (OME) is the retrograde movement of bacteria from the oropharynx into the middle ear cavity. OME is one of the most common causes of hearing loss in children. We have used a PCR-based method to identify Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola and Fusobacterium nucleatum in 65 middle ear effusion (MEE) samples obtained from paediatric patients seen for myringotomy and tube placement. DNA was extracted from MEE samples and PCR was initially done with DNA extracts by using the universal primers within the 16S rRNA gene sequence common to all bacterial species. The positive samples were further assessed with four species-specific primers. With the universal primers, 27 of 65 samples (41.5%) showed positive reaction indicating the presence of bacterial DNA. F. nucleatum was present in 10 out of 27 PCR-positive samples (37%) while one sample was positive for both T. denticola and F. nucleatum (3.7%). A. actinomycetemcomitans and P. gingivalis were not detected in any of the samples. The results of this study suggest that oral bacterial species may also play a role in the aetiopathogenesis of paediatric MEE. (C) 2001 Academic Press.