This study is the first to provide an extensive overview of the microbiology of acute ear, nose and throat infections requiring hospitalisation. All 2,028 cases of acute infections admitted between 1 January 2001 and 31 December 2006 were reviewed to assess the use of pre-admission antibiotics, microbiological results, antibiotic and surgical management and length of hospitalisation. Infections of the oropharynx accounted for the vast majority of admissions, followed by ear infections, and cutaneous neck abscesses. Peritonsillar abscess was the most frequent diagnosis, accounting for over one third of admissions (39.8%, 808 out of 2,028). Complete microbiological data were available for 1,430 cultures, and were analysed for trends with respect to diagnosis, age, gender and use of pre-admission antibiotics. Forty-six percent (657 out of 1,430) of cultures yielded no growth or normal flora. This value increased to 77.0% (298 out of 387) in patients with pre-admission antibiotics. The distribution of microbiological isolates varied significantly between patients with and without pre-admission antibiotics, as well as with respect to age and gender. The most frequently isolated bacteria were Group A Streptococcus (13.7%, 196 out of 1,430), Fusobacterium necrophorum (13.6%, 195 out of 1,428) and Staphylococcus aureus (8.0%, 114 out of 1,430). Fusobacterium necrophorum was primarily isolated from cases of peritonsillar abscess (90.8%, 177 out of 195). This study suggests that F. necrophorum is a far more widespread pathogen in otorhinolaryngology than previously reported, and questions the value of routine culturing, as results rarely altered initial treatment. Further research on the microbiological variations with age and gender is recommended to better target culturing and treatment, and enhance our understanding of the pathogenesis of ear, nose and throat infections.