Peritonsillar abscesses (PTA) are polymicrobial infections, with a diverse aerobic and anaerobic flora. The aim of the present study is to compare bacteriologic culture results from patients with PTA to those from patients undergoing elective tonsillectomy (clinically non-infected tonsils), to better elucidate the pathogenic significance of various isolates. A prospective study was conducted on 36 PTA patients undergoing acute tonsillectomy and on 80 electively tonsillectomised patients. Fusobacterium necrophorum (FN) and Streptococcus group A (GAS) were isolated significantly more frequently from the tonsillar cores of PTA patients, from both the abscessed (p = 0.001 and p = 0.046, respectively) and non-abscessed sides (p < 0.001 and p = 0.046, respectively), than from the tonsillar cores of electively tonsillectomised patients. Our findings indicate that FN and GAS are the prominent pathogens in PTA. In patients with PTA, the incidence of FN and GAS isolated from the abscessed tonsil was the same as from the non-abscessed contralateral side, and the growth was comparable by a semi-quantitative approach. Our findings suggest that FN is also of pathogenic importance in acute tonsillitis, and that FN growth is not a subsequent phenomenon once an abscess has formed. Our findings further suggest that other factors influence the development of PTA.