Recent work suggests Pseudomonas aeruginosa (Pa) infections usually persist after ETI, but mechanisms of post-ETI infection are unknown. A leading hypothesis posits that lung segments with mild structural damage will clear infection, while those with severe damage will remain infected. To test this, we performed bronchoscopy in 9 adults with ΔF508 CFTR. CTs identified the 2 most- and 3 least-severely damaged lung segments in each subject. All 5 segments were lavaged before and 1.5 years after ETI. Before ETI, 43/45 segments were Pa-positive. After ETI, average Pa density declined 2.3 log10 CFU/mL. However, 6 subjects remained infected. In these subjects, nearly all high and low-damage segments remained Pa-positive. This finding contradicts the hypothesis that infection persists only in high-damage lung segments.