Aim:The study was designed to investigate the sealing ability of two obturation systems (cold laterally compacted gutta percha and Obtura II) over different apically separated rotary nickel-titanium files (RACE and K3 system) using dye extraction method.Materials and Methods:Sixty-two mandibular premolars were divided into 2 groups of 30 teeth each, and 2 teeth served as negative controls. In Groups A and B, roots were prepared using RACE and K3 system, respectively, and were further subdivided into 4 subgroups. In subgroups A1, B1 and A2, B2 (n = 10 each), files were separated at 3 mm from the tip in apical 3rd of the canal. In subgroups A3, B3 and A4, B4 (n = 5), instruments were not separated. Subgroups A1, A3, B1, B3 and A2, A4, B2, B4 were obturated by lateral condensation method and Obtura II techniques, respectively. The sealing ability of the obturated specimens were tested using dye extraction method. The values for each group were recorded and analysis of variance (ANOVA), Student “t” test (two-tailed, independent), and Leven's test were performed.Results:Group A1 showed significantly less leakage than B1. No statistical significant difference between Groups A2 and B2 and Groups A3 and B3, respectively, were observed. Group A4 showed significantly less leakage than B4.Conclusion:Groups obturated with Obtura II showed less leakage than the lateral condensation technique irrespective of presence or absence of fractured NiTi rotary system.