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During 1991 to 1998 at least one Stenotrophomonas maltophilia pulmonary infection was observed in 25 (24%) of 104 cystic fibrosis (CF) patients at the same unit of our hospital in Spain. Ribotyping and pulse-field gel electrophoresis (PFGE) characterization of 76 S. maltophilia isolates from these patients indicated an overall clonal incidence of 47.1%, reflecting new strains in 44% of patients with repeated positive cultures for S. maltophilia. Six patients with repeated episodes were persistently colonized (>6 months) with the same strain. S. maltophilia bacterial counts were higher (geometric mean, 2.9 x108 cfu/mL) in patients with repeated episodes than in those with a single episode (8.4 x104 cfu/mL, p16 years of age).