Background: Longtime follow-up studies on patients with pharyngotonsillitis are rare. We aimed to describe the patterns of new visits for a sore throat, complications and tonsillectomy during 2 years in a cohort of patients with pharyngotonsillitis and non-infected controls. Methods: A retrospective chart review was performed on a cohort of patients with acute sore throat (n = 207), and non-infected controls (n = 108). New visits, complications and tonsillectomy within 2 years was recorded and analyzed in relation to microbiological findings at inclusion. Results: Patients with Group A streptococci (GAS) (12/66) reconsulted more often within 30 days than patients with no GAS (9/141) (p = 0.009) and patients with F. necrophorum (2/29). After 2 years, we observed no significant differences in reconsultations with regard to aetiology at inclusion. A single complication was recorded and 5 patients were planned for tonsillectomy. Conclusions: Group A streptococci were the sole aetiological agent associated with recurrent sore throat while F. necrophorum did not distinguish itself as a major cause of either recurrent infection or complications in this cohort. More studies, preferably with the focus on adolescents, are needed before F. necrophorum can be considered an important cause of pharyngotonsillitis.