Like many other Gram-negative bacteria, Burkholderia cepacia naturally releases membrane vesicles (n-MVs) during normal growth. Through filtration and differential centrifugation, n-MVs from clinical isolates of the IIIa and V genomovars were isolated and their characteristics compared. Electron microscopy revealed that they were spherical, 30-220 nm in diameter, and bilayered. Virulence factors thought to play a role in pathogenicity (e.g., lipase, phospholipase-N, and protease, including a metalloprotease) were found associated with n-MVs, while peptidoglycan zymogram analysis also revealed 26, 28, 36, and 66 kDa peptidoglycan-degrading enzymes. n-MVs were often contaminated with flagella and pili when isolated by traditional methods, and a new strategy using a linear isopycnic sucrose gradient was utilized. For better characterization, this was applied to a representative genomovar IIIa strain (C5424) and showed that n-MVs consisted of a subset of specific outer membrane and periplasmic proteins as well as lipopoly saccharide possessing only a putative minor O-side chain polymer. This finding suggests that certain components are selected by B. cepacia during n-MV formation, and since some are putative virulence factors, this property could help deliver the factors to tissue, thereby aiding infection.