Lung transplantation (LT) is the last-resort treatment to the lung destruction due to chronic infections in cystic fibrosis (CF) patients. However, Pseudomonas aeruginosa, a bacterium causing chronic infections in adult CF patients, is able to colonize the allograft within the first days after the LT. Seeding from the sinuses, the bacterium rapidly invades the donor flora and establishes as the dominant species. How CF-adapted P. aeruginosa strains achieve to drastically outcompete the lung donor microbiota remains unclear. The first cluster of the type VI secretion system (H1-T6SS) is frequently used by P. aeruginosa to counterattack other T6SS-producing Gram-negative bacteria. We hypothesized that T6SS can be involved in the ability of P. aeruginosa to outcompete the lung donor flora after transplantation. We first developed an appropriate method to evaluate the T6SS phenotype of clinical P. aeruginosa isolates in competition with an Acinetobacter baylyi reporter strain. We then screened a wide library of clinical P. aeruginosa isolates from 6 lung-transplanted CF patients and characterized their T6SS phenotypes. We also evaluated the T6SS phenotypes of non-CF isolates collected from 17 intubated patients. Screening of CF-adapted clinical isolates revealed that positive selection occurred in 4 out of 6 CF-patients screened. We observed a positive selection of T6SS producers in 2 patients, and of T6SS non-producers in 2 patients, whereas in the 2 others patients, no evidence of T6SS producer was reported neither before nor after LT. This highlighted a large diversity of T6SS phenotypes among clinical isolates. A similar diversity was also reported in non-CF adapted isolates collected from intubated patients. In conclusion, this study is the first screening of clinical isolates for the T6SS phenotype. This work contributes to elucidate bacterial competition taking place in the lungs.