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Pulmonary infections continue to be a significant source of morbidity and mortality among patients with cystic fibrosis. Although our understanding of the pathogenesis and clinical consequences of pulmonary infections with Pseudomonas aeruginosa has increased greatly in recent years, very little is known about potentially emerging pathogens such as Burkholderia cepacia complex, Stenotrophomonas maltophilia, Alcaligenes xylosoxidans, and methicillin-resistant Staphylococcus aureus. In this review, the authors discuss methods for appropriate identification of these “unusual” organisms and their epidemiologic and clinical features. Multicenter surveillance studies are needed to more clearly establish the pathogenicity of these organisms.