The aim of this study was to assess the cleaning capacity of the Protaper system using motor-driven or manual instrumentation. Materials and Methods: Ten mandibular molars were randomly separated into 2 groups (n = 5) according to the type of instrumentation performed, as follows: Group 1 - instrumentation with rotary nickel-titanium (Ni-Ti) files using ProTaper Universal System (Dentsply/Maillefer); and, Group 2 - instrumentation with Ni-Ti hand files using ProTaper Universal (Dentsply-Maillefer). Afterwards, the teeth were sectioned transversely and submitted to histotechnical processing to obtain histological sections for microscopic evaluation. The images were analyzed by the Corel Photo-Paint X5 program (Corel Corporation) using an integration grid superimposed on the image. Results: Statistical analysis (U-Mann-Whitney - P < 0.05) demonstrated that G1 presented higher cleaning capacity when compared to G2. Conclusions: The rotary technique presented better cleaning results in the apical third of the root canal system when compared to the manual technique.