BACKGROUND: A substantial proportion of patients become colonized with Candida spp. after surgery, but only a minority subsequently develop invasive candidiasis. However, clinical signs of severe infection manifest only late, presenting a challenge for diagnosis. Better knowledge of the pathogenesis of candidiasis and new compounds have improved the prognosis but also encouraged the emergence of non-albicans strains of Candida. DIAGNOSIS: Genotyping has confirmed that colonization from endogenous sources is responsible for the majority of cases of invasive candidiasis. Nevertheless, even if a large proportion of surgical patients becomes colonized, only a minority develop invasive candidiasis. This subgroup is difficult to identify, and many clinicians treat systematically all colonized patients, a practice that may select resistant strains. Biological tools have not improved the diagnosis, and the threshold between colonization and infection remains to be determined. The colonization index, defined as the ratio of the number of sites colonized by Candida strains to the number of sites tested, is a useful tool. CONCLUSIONS: After surgery, empiric treatment must be restricted to patients in whom the dynamics of Candida colonization predict a very high risk of invasive candidiasis. Prophylaxis should be limited to the small group of patients in whom its efficacy is proven.