The aim of this prospective study was to investigate the association between Candida spp. isolated from blood culture and the colonisation of different anatomical sites of patients with candidemia, and to evaluate the colonisation dynamics and Pittets index. Cultures were collected from the different anatomical sites of all the patients within 24 h of diagnosis of candidemia. Molecular similarities between identical species colonised with Candida species were evaluated via karyotyping. The colonisation index, as developed by Pittet et similar to al. was calculated using screening culture results from patients. Among the 40 patients screened for colonisation, 35 (87.5%) had colonisation of at least one anatomical site. Twenty-six (74.3%) of the 35 patients with colonisation in any of the three anatomical sites (respiratory, rectum and urinary sites) were shown to be colonised with the same species that caused candidemia. When the anatomical sites were compared with each other, no significant difference was observed at the species level in terms of colonisation index. The colonisation index (=0.5) positivity rate was 74% in patients with candidemia. The investigation of Candida colonisation of at least three anatomical (respiratory, rectum and urinary) sites could help in the selection of empirical antifungal therapy when nosocomial candidemia is suspected.