Catheter-related bloodstream infection (CRBSI) is one of the most serious complications in hospitalised patients, leading to increased hospitalisation, intensive care admissions, extensive antibiotic treatment and mortality. A greater understanding of these bacterial infections is needed to improve the prevention and the management of CRBSIs. We describe here the systematic culture-independent evaluation of intravascular catheter (IVC) bacteriology. Twelve IVCs (6 central venous catheters and 6 arterial catheters) were collected from 6 patients. By using traditional culture methods, 3 patients were diagnosed with catheter colonisation including 1 patient who also had CRBSI, and 3 had no colonisation. From a total of 839,539 high-quality sequence reads from high-throughput sequencing, 8 microbial phyla and 76 diverse microbial genera were detected. All IVCs examined in this study were colonised with complex microbial communities including “non-colonised IVCs,” as defined using traditional culture methods. Two main community types were observed: Enterobacteriaceae spp., dominant in patients without colonisation or CRBSI; and Staphylococcus spp., dominant in patients with colonisation and CRBSI. More diverse pathogens and a higher microbial diversity were present in patients with IVC colonisation and CRBSI. Community composition did not appear to be affected by patients’ antibiotic treatment or IVC type. Characterisation of these communities is the first step in elucidating roles of these pathogens in disease progression, and to ultimately facilitate the improved prevention, refined diagnosis and management of CRBSI.