We conducted a study to assess the precise incidence of anaerobic infections among patients with pulmonary diseases in Japan. To avoid false-negative results of anaerobic cultures, we used percutaneous transtracheal aspiration and subsequent immediate bedside anaerobic inoculation onto a set of plates with appropriately selected culture media. Fifty-six episodes of pulmonary disease occurred in 50 patients; anaerobes were isolated in 20 (36%) of these episodes. Bacteria were recovered in 30 (94%) of 32 episodes not associated with prior antimicrobial therapy, and anaerobes were isolated in 15 (47%) of these 32 episodes. Rates of anaerobic isolation in episodes of pneumonia (7 of 14), lung abscess (3 of 3), and acute exacerbation of chronic lower respiratory tract infection (5 of 15) that were not associated with prior antimicrobial therapy were 50%, 100%, and 33%, respectively.