Erythromycin and clindamycin are currently recommended for antibiotic prophylaxis of infective endocarditis in predisposed patients allergic to penicillin undergoing oral invasive procedures. Thirty-eight healthy patients were randomized to receive either erythromycin (1 g) or clindamycin (0.6 g) orally 1.5 h prior to dental extraction. Blood samples for microbiological investigation were collected before, during and 10 min after surgery and were processed by lysis filtration under anaerobic conditions. The incidence of bacteraemia with viridans streptococci was 79% in the erythromycin group and 74% in the clindamycin group. No statistically significant difference was noted in incidence or magnitude of bacteraemia with viridans streptococci or anaerobic bacteria between the two groups, at any sampling time. Ninety-six aerobic and 133 anaerobic strains recovered from the blood samples were tested for their susceptibility to erythromycin and clindamycin as well as to penicillin V and ampicillin. The antimicrobials were found to be highly active against the majority of bacteria except for some enterococci, staphylococci and veillonella. Protection from endocarditis by prophylaxis with erythromycin or clindamycin must be due to elimination of bacteria at a later stage in the development of the disease, rather than by elimination of bacteria from blood during the short period of postoperative bacteraemia.