Recurrent tonsillitis is 1 of the common human infectious diseases worldwide, but, to date, its pathogenesis remains unclear. Although Streptococcus pyogenes (GAS) is involved in recurrent bouts of acute tonsillitis, conventional cultures usually fail to isolate it. The purpose of this study was to clarify whether the deep tonsillar tissues of patients with recurrent tonsillitis might harbour GAS, resulting in reinfections. Deep tonsillar tissues obtained from 285 patients with recurrent tonsillitis and 172 patients with tonsillar hypertrophy, who had undergone tonsillectomy, were examined for the presence of GAS, using conventional and molecular methods. Cultures from all patients were negative for GAS. GAS DNA was found in the deep tonsillar tissues of 57 out of 285 patients with recurrences (20%), and GAS RNA, indicating the viability of GAS, was detected in 47 of them (82%). On the other hand, Haemophilus influenzae DNA was found in 15% and 16% of patients with recurrences and hypertrophy, respectively; but no Haemophilus influenzae RNA presence was detected. The low level of presence of GAS in patients with recurrent tonsillitis indicates that other unknown factors may be responsible for the recurrences.