This study evaluated the efficiency of using a single instrument from three different rotary multi-file systems and compared them with that of a reciprocating single-file for endodontic retreatment by means of micro-CT. Sixty extracted canines were prepared using a size F2 ProTaper Universal file and obturated. After 30 days of storage at 37ºC and 100% humidity, the teeth were randomly divided into four groups (n=15) based on the type of instrument used to retreatment: ProTaper Next (PTN), ProTaper Gold (PTG), TRUShape 3D (TS), and WaveOne (WO). The canals were retreated using only the size 40 instrument from each system according to the manufacturer's recommendations for torque and speed. The time required to remove the filling material was recorded in seconds. The amount of initial and residual filling material and the quantity of dentin removed were assessed by means of micro-CT. Data were statistically analyzed (ANOVA and Kruskal-Wallis) at a 5% significance level. TS instruments required the highest (p<0.05) amount of time (mean, 384.80 ±144.92) compared with the WO (229.67±68.16) and PTG (248.67±64.22) and not so different from PTN instruments (327.67±133.3). No differences in the amount of dentin removed, initial and residual filling volume, and percentages of filling material were observed among the groups. The use of a single rotary instrument from the PTG, TS, and PTN systems was as effective as that of the single-file reciprocating WO system. However, none of the instruments was able to remove the filling materials completely.