Wound infections resulting from contamination during major head and neck surgery continue to be a critical issue. In this study, specimens of pus or draining fluids from the wounds of 43 surgical patients who received perioperative administration of ampicillin/sulbactam or clindamycin were cultured for aerobic and anaerobic isolates to species level. Polymicrobial infections were identified in 13 of 43 patients (30%); 82% of isolates were aerobic organisms (45 of 55), and 18% were anaerobic or facultative species (10 of 55). Nine of 43 patients (21%) showed no bacterial isolates from cultured material. Independent of the primary site of malignancy or antibiotics used, nine of 25 isolates (36%) obtained from patients who underwent concomitant dental extractions, but only one of 24 (4%) who did not, developed anaerobic infections, (p < 0.001). The minimum inhibitory concentration of anaerobic isolates suggested sensitivity to the antibiotics used, and minimum bactericidal concentration data suggested that further postoperative doses may be required to adequately treat the heavily contaminated wounds. These data suggest that wound colonization following dental extraction procedures in clean contaminated head and neck surgery increases the risk of anaerobic infections. The use of a therapeutic dose and longer duration of perioperative antibiotics may be warranted.