Decreasing susceptibility to ciprofloxacin was investigated in sequential clinical isolates of Pseudomonas aeruginosa from a patient on ciprofloxacin therapy. All isolates were verified as the same strain by DNA probe. MICs of all quinolones tested were 16- to 32-fold higher for the posttherapy isolates; nonquinolone MICs were unchanged. The isolates were compared by analyses of outer membrane proteins and lipopolysaccharide composition, antimicrobial susceptibilities, measurement of accumulation of ciprofloxacin, and inhibition of DNA gyrase activity by ciprofloxacin and nalidixic acid. No significant changes in outer membrane proteins or ciprofloxacin accumulation were observed; however, both posttherapy isolates lost the long chain O-polysaccharide component of lipopolysaccharide. Preparations of DNA gyrase from the quinolone-resistant posttherapy isolates were 16- to 32-fold less sensitive to inhibition of supercoiling by ciprofloxacin and nalidixic acid than was gyrase from the pretherapy isolate. Inhibition studies on combinations of heterologous gyrase subunits showed that decreased inhibition was conferred by the resistant gyrase A subunits. Thus, acquired resistance to ciprofloxacin in this strain involved an alteration in the A subunit of DNA gyrase and was associated with changes in lipopolysaccharide.