OBJECTIVE To compare the cultures of tonsillar surface aerobic and anaerobic bacterial flora taken during the acute phase of infectious mononucleosis with the repeated cultures taken 2 months later. METHODS Fourteen patients with pharyngotonsillitis associated with infectious mononucleosis. RESULTS A total of 121 bacterial isolates (ie, 84 anaerobes and 37 facultatives and aerobes) were isolated in the acute stage, and 75 isolates (ie, 42 anaerobes and 33 aerobes) were recovered 2 months later. The reduction in the number of organisms in the second specimen was mostly due to the decrease in the recovery of Prevotella intermedia (13 in the first culture, compared with four in the second) and Fusobacterium nucleatum (12 vs four, respectively). CONCLUSIONS The study illustrates that the surfaces of tonsils of patients with infectious mononucleosis contain more species of anaerobic organisms during the illness than following it. The potential role of these organisms in the inflammation process warrants further study.