In order to reduce errors during root canal preparation, there have been several changes in instrumentation with rotatory systems of nickel-titanium. This is an in vitro study and the aim was to compare the degree of transportation that occurs at the union between the apical third and half third of root canals with the rotaroty Protaper Universal and nickel titanium manual system with balanced force technique. We worked with 52 mesial canals of 26 first and second maxillary and mandibular molars, which were divided into two groups. The first group (n = 28) was instrumented with rotary Protaper Universal and the second group (n = 24) was instrumented with manual technique with balanced force. The mesial roots of molars were immersed in a matrix of acrylic, which allowed manipulating the preparations with transversal cuts and comparing the wear of the root canals before and after the instrument to set the differences were observed in the apical transport. The images obtained were photographed with a stereoscopic microscope and analyzed with the Autodesk AutoCAD® 2007. Finally, the data were tabulated and analyzed with Stata® V.9.0. Protaper Universal rotatory results showed a decreased apical transport compared with the manual technique with balanced forces.