Background: Stainless steel instruments have long used as conventional instruments applied in root canal therapy procedures. Being difficult the canal preparation by these instruments, a new generation of nickel-titanium instruments have introduced. The aim of this study was to compare the manual Ni-Ti instruments with the Flex Master® Ni-Ti rotary system in canal preparation.   Materials & Methods: Fifty patients having maxillary or Mandibular first or second molar teeth were selected and were divided in to two separate groups containing 25 patients each. After preparing the access cavities and placing No.15 manual Ni-Ti files within the canals, a periapical radiograph was taken by the means of Endo-ray®. In the group I, canal preparation was done through crown-down technique and manual Ni-Ti K-Flex files in which the coronal two thirds of the canals were prepared by stainless steel Gates Glidden drills. In the group II, the instrumentation procedure was performed by the means of rotary Ni-Ti Flex Master® system regarding the manufacturer’s instructions. After the instrumentation, a periapical radiograph was taken by Endo-ray®. All the pre- and post-treatment radiographs were digitized by the use of Fine Pix Fuji film® digital camera equipped by macro 50x lens and 2.8 diaphragm. The initial and post-treatment angulations of the canals, the amount of ledge formation, the occurrences of transportations, internal or external inclinations of the canal walls, root perforations and broken files were evaluated by Demo® and Adobe Photoshop < sup>® 7 computer soft wares.   Results: In group II, The canals were significantly more centrally located than those in group I and indicated less occurrence of transportation and no incidence of ledge formation. There was no perforation in either of the groups and not a significant interrelationship between the broken instruments and any of the methods used. Conclusion: Generally, the Ni-Ti rotary Flex Master® system can be a suitable choice in root canal preparation procedures.