This study investigated the sealing properties of cold laterally compacted gutta percha and Thermafil applied over different apically fractured rotary nickel-titanium files. Extracted human premolars were prepared by using ProTaper (Dentsply-Maillefer, Ballaigues, Switzerland) or ProFile (Dentsply-Maillefer) systems (n = 40 for each), after which half of the specimens in each subgroup were subjected to instrument separation at the apical level. For each rotary system, roots with and without apically separated instruments (n = 10 for each) were filled with the two obturation systems and the levels of fluid conductance were recorded, In the absence of instrument separation, the leakage of Thermafil (Dentsply Maillefer) was significantly less than that achieved with cold lateral compaction (p < 0.05), whereas Thermafil yielded similar amounts of leakage in roots prepared with the ProTaper and ProFile systems (p < 0.05). Roots with fractured ProTaper instruments displayed significantly less leakage than those filled without ProTaper fragments, regardless of the obturation technique used (p < 0.05). However, intracanal separation of ProFile instruments increased the leakage (p < 0.05), but the obturation method did not influence fluid conduction (p > 0.05). These results reveal the variability of leakage associated with apically fractured ProFile and ProTaper files and different obturation methods used.