BackgroundMicrobiological identification in endodontic infections has focused mainly on bacteria without giving much attention to yeasts, which, due to their virulence factors, can affect the outcomes of root canal treatment. AimsTo determine the frequency of Candida in anaerobic conditions in root canals with primary and persistent endodontic infection, as well as to evaluate a microbiological sampling method using aspiration compared to the traditional absorption method with paper points. MethodsFifty microbiological samples were obtained from teeth of 47 patients requiring endodontic treatments, due to either primary or persistent infections. Two microbiological sampling methods were used: an aspiration method, and the traditional paper point absorption method. In each of these methods, two types of medium were used (M1-M4). Samples were cultured under anaerobic conditions until reaching 0.5 McFarland turbidity, and then inoculated on Sabouraud dextrose, as well as on anaerobic enriched blood agar plates. Macroscopic and microscopic observations of the colonies were performed. The germ-tube test, growth on CHROMagar, and biochemical identification were performed on the isolated yeasts. ResultsFungal infection was found in 18 (36%) samples out of the 50 teeth evaluated. In the 18 samples positive for fungal infection, 15 out of 36 (41.6%) teeth were taken from a primary infection, and 3 out of 14 (21.4%) from a persistent infection. The aspiration method using Sabouraud dextrose medium recovered a greater diversity of species. ConclusionsYeasts frequency was higher in teeth with primary infections compared to teeth with persistent infections. The predominant yeast species was Candida albicans. The aspirating sampling method was more efficient in the recovery of Candida isolates than the traditional absorption method.