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The impact of minimally invasive endodontic procedures on root canal disinfection has not been determined. This ex vivo study compared root canal disinfection and shaping in teeth with contracted or conventional endodontic cavities.Mandibular incisors with oval-shaped canals were selected and anatomically matched based on micro–computed tomographic (micro-CT) analysis and distributed into 2 groups. Conservative and conventional access cavities were prepared, and the canals were contaminated with a pure culture of Enterococcus faecalis for 30 days. Root canal preparation in both groups was performed using the XP-endo Shaper instrument (FKG Dentaire, La Chaux-de-Fonds, Switzerland) and 2.5% sodium hypochlorite irrigation. Intracanal bacteriologic samples were taken before and after preparation, and DNA was extracted and subjected to quantitative polymerase chain reaction. Micro-CT scans taken before and after preparation were used for shaping evaluation. Bacteriologic data were analyzed by the Poisson regression model and the chi-square test with Yates correction. Micro-CT data were analyzed by the Wilcoxon, Mann-Whitney, and Student t tests with the significance level set at 5%.All initial samples were positive for E. faecalis. After preparation, the number of bacteria-positive samples was significantly higher in the contracted cavity group (25/29, 86%) than in the conventional cavity group (14/28, 50%) (P < .01). Intergroup quantitative comparison showed that the reduction in bacterial counts was also significantly higher in the group of conventional cavities (P < .01). Micro-CT data revealed no significant difference in the amount of unprepared areas between groups.Our findings showed that although shaping using an adjustable instrument was similar between groups, disinfection was significantly compromised after root canal preparation of teeth with contracted endodontic cavities.