Members of the Burkholderia cepacia complex (Bcc) can cause disease or can be beneficial for plants. The Bcc bacteria are nutritionally diverse and can grow in diverse environments; some can even degrade important pollutants or can use penicillin G as a sole source of carbon.Bcc bacteria can act as opportunistic pathogens and are associated with a variable clinical course in patients with cystic fibrosis (CF) that can include severe lung infections, necrotizing pneumonia and septicaemia.The Bcc currently includes nine species (genomovars). The most common species that cause infections in CF patients are B. cenocepacia (genomovar III) and B. multivorans (genomovar II).Epidemiological studies have identified highly transmissible clones of Bcc bacteria, some of which have been associated with serious outbreaks among CF patients. One of the most prevalent belongs to the ET-12 lineage.However, the factors responsible for the transmission and virulence of these or other epidemic strains have not been identified. It is suggested that, in addition to bacterial factors, the host response is responsible for the variable clinical course among patients.The availability of genome sequence data for the ET-12 lineage strain B. cenocepacia J2315 has led to the identification of novel genomic islands and facilitated the development of genetic tools to investigate the pathogenesis of this bacterium.These tools have been exploited, along with various models systems that include infections in cell cultures, animals, plants, worms, and amoebae, which have led to the identification and characterization of potential virulence factors.