To systematically review all studies comparing manual instrumentation with at least one rotary instrument in the preparation of the root canal of permanent human teeth.The electronic databases PubMed, EMBASE, LILACS, IBECS and BBO were searched. In vitro studies published until 27 of September, 2016 were included. For statistical analysis, we used the Comprehensive Meta-Analysis software (Biostat), considering P< 0.05 significant.A total of 1,104 articles published until September 27, 2016 were obtained, with 57 meeting the eligibility criteria. The studies were grouped according to the main methodology used (computerized tomography, periapical radiography, image amplification and scanning electron microscope). Due to the wide variability of the methodologies and evaluated parameters, a subgroup analysis was performed based on the evaluated parameter. The meta-analysis revealed that rotary instruments caused a significant reduction in instrumentation time and a smaller change of the canal curvature than manual instruments. The rotary instrumentation presented better results regarding root canal transportation, ability of centralization within the canal path and shaping of the canal. Manual instrumentation performed better with regard to the smear layer and debris production, more instrumented canal surfaces and fewer dentin defects.An increasing number of studies have compared the efficiency of manual and rotary instrumentation in endodontic treatment of permanent teeth. This study helps elucidate which method is more efficient in the endodontic treatment of permanent teeth.