A novel method for the in vitro culture of tissue biopsies is presented. Infected tonsillar biopsies were successfully cultured by means of the continuous flow of media without the addition of antibiotics. Histological and immunohistological examinations were carried out on sections of Streptococcus pyogenes-infected cultured tonsillar biopsies and sections from the surgically removed tonsils of asymptomatic S. pyogenes carriers. Low numbers of intracellular S. pyogenes were detected inside epithelial cells in eight out of 12 (67%) S. pyogenes-infected biopsies, and in four out of 11 (36%) tonsils of asymptomatic carriers. Our findings support the hypothesis that the sanctuary where S. pyogenes avoids antibacterial treatment is intracellular, which may provide a possible explanation of recurrent tonsillitis.