Differentiating reinfection from the acquisition of resistance in strains of Pseudomonas aeruginosa after antimicrobial therapy is difficult because currently used epidemiological markers are not stable genetic markers. We previously established that a 741-base pair PstI-NruI restriction fragment upstream from the Exotoxin A structural gene is a sensitive, specific, and stable epidemiological marker for P. aeruginosa. Therefore, we used this fragment as a probe in Southern hybridization to compare pre- and post-therapy isolates of P. aeruginosa. The susceptible and resistant pairs were recovered from multiple sources (including sputum, blood, and urine) from patients treated with various doses of imipenem (n = 15), norfloxacin (n = 6), and ciprofloxacin (n = 4). Southern blot analysis showed identity between the pre- and post-therapy isolates in 23 of the 25 pairs. In the majority of pairs studied, failure to eradicate P. aeruginosa after therapy with imipenem, norfloxacin, and ciprofloxacin was due to the development of resistance rather than to reinfection.