Background Over 80% of children experience acute otitis media (AOM) at least once during childhood, with 10-30% of children experiencing recurrent episodes of AOM (RAOM) or persistence of fluid in the middle ear (ME) lasting greater than 3 months which is defined as chronic otitis media with effusion (COME). Microbial infection remains the main cause of AOM, however the causes of RAOM and COME are not fully understood. Heavy loads of microbial colonisation and bacterial/viral interaction in the upper respiratory tract (URT) contribute to OM pathogenesis. It is currently unclear whether compromised host immune system responses have a significant role in RAOM/COME. Bacterial biofilms within the ME may contribute to otopathogen persistence and recurrent infection and/or inflammation in these children. Aims This study identified the predominant bacterial and viral otopathogens within the URT and ME, of children undergoing ventilation tube insertion (VTI) for RAOM/COME. Bacterial persistence within the ME, in the form of biofilms was also examined. Bacteria and viruses which were identified within the URT of children with RAOM/COME were compared to a control group of children who were undergoing adenoidectomy for treatment of adenoidal hypertrophy (AH) and/or obstructive sleep apnoea (OSA). Local (saliva, middle ear effusion (MEE)) and systemic (serum) innate and adaptive immune responses were examined in children with and without RAOM/COME. Specific antibody levels to bacterial proteins as well as cytokine levels were determined. Systemic immuno-gene expression was compared between children with RAOM/COME and AH/OSA.