The interaction of over 100 isolates of Pseudomonas aeruginosa representing different genotypes of type III secretion system (TTSS) with RAW 264.7 murine macrophage-like cells and pulmonary microvascular endothelial (PME) cells were studied. The strains were isolated from clinical materials and from stool specimens of healthy carriers and were analyzed by pulsed field gel electrophoresis (PFGE) to characterize their heterogeneity. In order to differentiate TTSS genotypes of P. aeruginosa isolates, the distribution of the following genes: exoU, exoS, pcrV, exoT, and exoY was assessed by multiplex and duplex PCR assays. The cytotoxicity and invasiveness of the P. aeruginosa isolates were determined. P. aeruginosa isolates showed a discrepancy in their ability to induce cytotoxicity and to invade mammalian cells. Up to four phenotypes among the isolates were observed and the most diverse interactions of the isolates were noticed with PME cells. The reduction of the viability of the cells, infected by P. aeruginosa isolates of the same clone, was associated with the ability of these strains to secrete the TTSS effectors: ExoU or ExoS. The results of this study also suggest that healthy people can be the carriers of cytotoxic strains of this dangerous pathogen.