- The optimal methodology for the identification of colonization by potential respiratory pathogens (PRP) in adults is not well established. The objectives of the present study were to compare the sensitivities of sampling the nasopharynx and the oropharynx for identification of PRP colonization and to compare the sensitivities of samples from the nasopharynx by swab and by washing for the same purpose. The study included 500 participants with a mean age of 65.1 ± 17.8 years. Of these, 300 patients were hospitalized for acute febrile lower respiratory tract infection and 200 were controls. Each participant was sampled by oropharyngeal swab (OPS), nasopharyngeal swab (NPS), and nasopharyngeal washing (NPW). The samples were tested by conventional bacteriological methods to identify Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. OPS detected colonization by S. pneumoniae in 30% of the subjects compared with 89% by NPS and NPW (P < 0.000001). The corresponding rates for H. influenzae were 49% and 64%, respectively (no significant difference [NS]), and for M. catarrhalis were 72% and 46%, respectively (P < 0.0004). NPS identified 61% of the cases of colonization with S. pneumoniae, compared with 76% by NPW (NS). The corresponding rates for H. influenzae were 31% and 56%, respectively (P < 0.04), and for M. catarrhalis were 39% and 33%, respectively (NS). We conclude that the sensitivities of nasopharyngeal and oropharyngeal sampling for identification of PRP colonization in adults are different for each of the three bacteria in this category. The combined results of sampling from both sites are necessary to obtain a true picture of the rate of colonization. NPW is superior to NPS.