This study aimed to compare the children having enlarged adenoids with and without otitis media with effusion (OME) concerning clinical features like mouth breathing, snoring, recurrent episodes of cold, hearing impairment and specific morphology of adenoid. Further, the flora of adenoid tissue and middle ear fluid were also compared. One hundred and twenty children having clinical features suggestive of enlarged adenoids with [Group A (n = 60)] or without [Group B (n = 60)] OME were included in this cross-sectional study. All patients underwent clinical examination, diagnostic nasal endoscopy, radiography of the nasopharynx, blood absolute eosinophil count and immittance. Core adenoid tissue was subjected to microbiological culture after adenoidectomy. OME fluid was subjected to microbial analysis after myringotomy. In group A patients, snoring was present in 90% (p = 0.011), adenoid facies in 76.6% (p < 0.001) and tubal tonsil enlargement in 86.7% (p < 0.001). The parts related to the development of OME were: behind the posterior cushion in 86%, touching the posterior end of septum in 76.7%, inside nasal cavity in 70% and completely covering the Eustachian tube orifices in 95% (p < 0.001 in all of them). Specific morphology of adenoid enlargement and tubal tonsil enlargement was more critical in predicting the risk of developing OME and not just the grade of adenoid hypertrophy. The microbial flora in the adenoid core was similar in children with and without OME.