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.Department of Endodontics, School of Dentistry, Federal University of Amazonas, Manaus, AM, BrazilDental Materials and Prosthodontics, Ribeirão Preto School of Dentistry, University of São Paulo, Ribeirão Preto, SP, BrazilUniversidade Estadual Paulista Júlio de Mesquita Filho, Departamento de Odontologia Restauradora, Faculdade de Odontologia de Araraquara, Araraquara, Rua Humaitá, 1680, Centro, CEP 14801-903, SP, Brasil