BACKGROUND: Premature neonates who have airway colonization with UU have been shown to be at increased risk for the development of chronic lung disease of prematurity (CLD). Pulmonary infection with UU may be the cause of CLD in some neonates and early diagnosis and appropriate antimicrobial therapy may be necessary to prevent the development of this condition. Current culture techiques for the isolation of UU are expensive, time consuming and labour intensive. Detection of UU components by PCR may allow rapid detection of even a small innoculum. METHODS: As part of a randomized trial to evaluate Alpha-1 Antitrypsin supplementation for the prevention of CLD, ETT aspirates taken on days 0, 4 and 14 were cultured for UU and examined by PCR. The PCR-based test used primers directed against a gene encoding a serodominant multiple-banded antigen. RESULTS: 225 ETT aspirates from 103 neonates (1-4 per patient) were examined. Of 77 specimens from 38 patients positive by either method, 73 were positive by PCR and 60 by culture. There were 17 specimens from 16 patients that were positive by PCR alone. In 13 of these patients (14 specimens), cultures were positive at another sampling point, and an additional patient had a twin that was culture positive, suggesting that at least 15/17 were true positive results. Of 11 patients with day 0 specimens positive by PCR alone, 9 subsequently became culture positive at a later time point. CONCLUSION: A PCR-based test appears to be more sensitive than standard culture techniques in identifying babies born prematurely who have airway colonization with UU. PCR may be particularly useful for early detection of patients with UU thus helping identify possible candidates for early antimicrobial intervention.(Funding received from Bayer/Canadian Red Cross Society Research and Development Fund)