The relation between carriage of Neisseria meningitidis and progression to invasive disease is not fully understood. We assessed the rate of N. meningitidis carriage by conventional swabbing and immunohistochemistry in patients undergoing tonsillectomy. Swabbing detected only a quarter of carriers, and bacteria were identified beneath the mucosal surface in tonsillar tissue by immunochemical testing. Our results indicate that N. meningitidis is more widespread in the population than previously thought, and have broad implications for disease prevention and cure.