Background: Bacterial infection, Eustachian tube dysfunction, allergies, and immunologic factors are major causes of otitis media with effusion (OME). However, the exact pathogenesis of OME is still unclear. This study evaluated whether allergy influences bacterial growth in middle ear effusions. Materials: Fifty-four samples were obtained from OME patients 3-10 years of age who underwent ventilation tube insertion and were divided into two groups based on the presence of allergy as determined using the multiple allergosorbent test (MAST). Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis bacterial DNA in the middle ear effusions was analyzed using polymerase chain reaction. Overall detection rates and those for each species were compared between the two groups. Results: Of the 54 middle ear effusion samples, 38 (70.4 %) contained bacterial DNA and 14 (36.8 %) of these contained DNA from multiple species. S. pneumoniae was detected in 27 samples (50 %), H. influenzae in 17 samples (31.4 %), and M. catarrhalis in 9 samples (16.6 %). There was no significant difference in the bacterial detection rates between the middle ear effusions of the MAST-positive and MAST-negative groups. Conclusion: The rate of bacteria detection in middle ear effusions did not differ between allergic and non-allergic children.