Statement of Problem: Due to the anatomic complextieis of C-shaped canals, using an obturation technique capable of filling the irregular isthmus in the root canal system seems to be necessary.Purpose: The aim of this study was to compare the efficacy of three different root canal obturation techniques used for filling the irregular root canal system in C-shaped teeth.Materials and method: The study was perfomed on 30 human extracted molar teeth which were radiographically and anatomically recognized as having C-shaped canals. All root canals were prepared in the same way and the samples were divided into 3 groups, each of 10 teeth. The root canals in group I were filled by cold lateral condensation technique (CL). Teeth in group II were filled by means of warm lateral condensation technique (WL) and those in group III were filled by means of warm vertical condensation technique (WV). All teeth were demineralized and then cleared with methylsalicilate. Images were taken from both longitudinal and cross-sectional feature of the cleared teeth by a digital camera connected to a stereomicroscope. The filling quality of the main canals and the isthmus between them was evaluated by three independent endodontists. The data were statistically analyzed by chi-square, one way and two way ANOVA and t-test.Results: In longitudinal photographs, the highest percentage of good filling quality (80%) was observed in the WV group and was significantly more acceptable than WL group (p<0.05). The lowest percentage of good filling quality was observed in the isthmus area of the canals (46.7%) which was significantly less than other areas (p<0.05). Cross- sectional photographs demonstrated no significant difference between the percentage of isthmuses filled with the filling material and the two areas of the canals in the three obturation techniques (p>0.05)Conclusion: The results indicated that none of the suggested techniques could successfully fill the root canal space, but the warm vertical and cold lateral condensation techniques were more acceptable than warm lateral condensation technique.Key words: C-shaped canals, Obturation quality, Obturation techniques, Molar teeth