The GroEL protein of Pseudomonas aeruginosa belongs to the bacterial 60–65 kDa heat shock protein family. A strong antibody response to GroEL has been found in cystic fibrosis (CF) patients with chronic pulmonary infection caused by P. aeruginosa. Clonotypes of IgG1 and IgG2 antibodies against GroEL were studied in 60 consecutive sera from 18 CF patients with chronic P. aeruginosa infection using isoelectric focusing in combination with affinity immunoblotting. The persistent antigenic stimulation in CF patients with chronic P. aeruginosa infection induced numerous IgG1 and particularly IgG2 antibody clones against GroEL. The appearance of new clones with time reflected the long duration of the chronic infection. A striking addition of new clonotypes during the observation period occurred when a new unrelated bacterium (Burkholderia cepacia) had become established as a cause of the pulmonary infection, or when the P. aeruginosa infection became chronic.