To study the incidence and magnitude of bacteremia after dental extraction and supragingival scaling. Blood samples were taken before and 5 and 30min after dental extraction and supragingival scaling from individuals at high (n=44) or negligible risk (n=51) for infective endocarditis. The former received prophylactic antibiotic therapy. Samples were subjected to aerobic and anaerobic culture and quantitative real-time polymerase chain reaction to determine the incidence of bacteremia and total bacterial levels. Patients who did not receive prophylactic antibiotic therapy had a higher incidence of positive blood cultures (30% 5min after extraction) than patients who received prophylactic antibiotic therapy (0% 5min after extraction; p<.01). Molecular analysis did not reveal significant differences in the incidence or magnitude of bacteremia between the two patient groups either 5 or 30min after each of the procedures evaluated. Extraction was associated with higher incidence of bacteremia than supragingival scaling by blood culture (p=.03) and molecular analysis (p=.05). Molecular methods revealed that dental extraction and supragingival scaling were associated with similar incidence of bacteremia in groups receiving or not prophylactic antibiotic therapy. However, blood culture revealed that antibiotic therapy reduced viable cultivable bacteria in the bloodstream in the extraction group.