Quorum sensing (QS) contributes to the virulence of Pseudomonas aeruginosa and Burkholderia cepacia complex lung infections. P. aeruginosa QS mutants are frequently isolated from patients with cystic fibrosis. The objective of this study was to determine whether similar adaptations occur over time in B. cepacia complex isolates. Forty-five Burkholderia multivorans and Burkholderia cenocepacia sequential isolates from patients with cystic fibrosis were analyzed for N-acyl-homoserine lactone activity. All but one isolate produced N-acyl-homoserine lactones. The B. cenocepacia N-acyl-homoserine lactone-negative isolate contained mutations in cepR and cciR. Growth competition assays were performed that compared B. cenocepacia clinical and laboratory defined wild-type and QS mutants. Survival of the laboratory wild-type and QS mutants varied, dependent on the mutation. The clinical wild-type isolate demonstrated a growth advantage over its QS mutant. These data suggest that there is a selective advantage for strains with QS systems and that QS mutations do not occur at a high frequency in B. cepacia complex isolates.