Lung disease is the direct cause of death in more than 90% of cystic fibrosis (CF) patients. Proteinase-antiproteinase imbalances are common in CF and alpha-1-antitrypsin (AAT) deficiency. We investigated the hypothesis that the AAT deficiency alleles PiS and PiZ contribute to pulmonary prognosis in CF. Two hundred and sixty-nine CF patients from Southern Germany were included in this study. The serum concentrations of AAT and C-reactive protein (CRP) were determined by nephelometry, and patients were screened by polymerase chain reaction (PCR) and restriction enzyme digest for the common AAT deficiency alleles PiS and PiZ. The onset of chronic bacterial colonization by Pseudomonas aeruginosa (Pae) was correlated with the AAT phenotypes PiMM, PiMS and PiMZ. Only three out of nine CF patients (33%) diagnosed with either PiMS or PiMZ had developed chronic Pae lung infection earlier in their lives. The remaining six patients showing a PiMS or PiMZ phenotype showed a later onset of chronic Pae lung infection. Our results indicate that PiMS and PiMZ are not associated with worse pulmonary prognosis in CF. These data need to be confirmed in studies with a much larger number of cases.