Background: allergic rhinitis is a common childhood disease responsible for a major impact on quality of life and health care resources. Many hypotheses have been proposed to explain the link between allergy and otitis media, although a definitive mechanism has not been identified yet. One of the major critical points is that authors failed in distinguishing among different phenotypes of middle ear inflammation. This review pointed out evidence from the laboratory and clinical experience to link allergy to different phenotypes of otitis media in children. Methods: we performed a systematic review in accordance with the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) process. Our search yielded 3010 articles that were finally screened. This resulted in 20 publications of which the full texts included for the qualitative analysis based on different phenotypes of otitis media. Results: clinical evidences and analyses of biomarkers suggested that allergy may be linked to some phenotypes of otitis media and, in particular, to otitis media with effusion and acute re-exacerbations in children with middle ear effusion. It was not possible to perform the analysis for allergy and acute and chronic otitis media because of paucity and heterogeneity of data. Conclusion: Allergy should be considered in the diagnostic work up of different phenotypes of otitis media. Clinicians should evaluate prompt and accurate treatment of allergy in improving outcomes, although futures studies are required to increase evidence supporting that anti-allergy treatment may be effective in the recovery and outcome of otitis media with effusion.