We aimed to determine whether there was a difference between core and surface bacteriology of Finnish adults with recurrent or chronic tonsillitis to understand whether a surface swab is worthwhile and which bacteria are involved. Case series. Uninflamed tonsillar surface swabs and core biopsies were taken prior to and during surgery, respectively, in 103 patients aged 16 to 66 years undergoing tonsillectomy for recurrent or chronic tonsillitis. The McNemar test was used to determine differences between the surface and core in the most prevalent bacterial species. Twenty-seven bacterial species were isolated in addition to normal flora and were more commonly found in the core (1.11 surface and 4.75 core bacteria isolated per patient). Viridans group streptococci were the most commonly detected bacteria, found in 88% of the patients, mainly in the core. The bacteria in general were mainly isolated from the core. Of the 10 most prevalent bacteria, only group C β-hemolytic streptococci showed no difference between detection from core and surface swabs. Other bacteria found mainly in the core include Prevotella melaninogenica, Staphylococcus aureus, and fusobacteria. There is discord between the surface and core bacteria. A different population of bacteria exists in the core, especially anaerobic bacteria, suggesting that a core sample may be useful in evaluating recurrent and chronic tonsillitis. 4 Laryngoscope, 2019.