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Background: The aim of our study was to determine the genotypes and antimicrobial susceptibility profiles of Pseudomonas aeruginosa isolates of cystic fibrosis (CF) patients. Methods: We included 18 P. aeruginosa isolates from 10 patients treated as in-patients or outpatients at University Clinic of Respiratory and Allergic Diseases Golnik between 1 January 2006 and 31 December 2008. Results: We determined 8 pulsotypes of P. aeruginosa. Pulsotypes A and C had 4 subtypes each. Different antimicrobial susceptibility patterns were observed in isolates with closely related macrorestriction profiles. Conclusions: We conclude that at a given time, patients with CF attending our clinic were colonized or infected with phenotypically and genotypically distinct strains of P. aeruginosa.