Throat swabs from 61 patients, aged 18-32 years, with non-streptococcal tonsillitis (NST) and 92 healthy controls were examined for the presence of Fusobacterium necrophorum DNA using a novel TaqMan-based real-time quantitative PCR assay for F. necrophorum subspecies. The assay was based on the gyrB subunit gene, and detected F. necrophorum DNA in 48% of patients with NST and in 21% of controls (p <0.001). F. necrophorum subsp. funduliforme was the only subspecies found in both patients and controls. The load of F. necrophorum DNA on swabs from patients with NST was significantly higher than that on swabs from controls (p <0.001). Furthermore, patients with recurrent NST had a significantly higher load of F. necrophorum DNA compared to patients with acute NST (p 0.04). In addition, 26 patients with tonsillitis and group C streptococci (GCS) had a significantly higher load of F. necrophorum DNA compared to the NST group (p <0.001). It was concluded that F. necrophorum subsp. funduliforme is present in small numbers as part of the normal human throat flora, and that F. necrophorum in large quantities may cause tonsillitis, especially recurrent tonsillitis. In addition, the study suggests that the concomitant presence of GCS may aggravate F. necrophorum tonsillitis.