The aim of the study was to compare the effect of Self-Adjusting Files (SAF) and WaveOne Primary file with syringe and needle irrigation on the filling ability of oval-shaped root canals obturated with thermoplasticized gutta-percha. Twenty-four single root teeth with single oval-shaped root canals were distributed into two experimental homogeneous groups. One group was instrumented and cleansed using the SAF system while in the other group the WaveOne system with syringe and needle irrigation was used. After instrumentation, the roots were filled by Thermafil Obturators and TopSeal sealer. Specimens were transversally sectioned at 2-, 5- and 7-mm levels from the apex and observed under light microscope. The percentage of gutta-percha filled area (PGFA), the percentage of sealer filled area (PSFA) and the percentage of voids area (PVA) were measured for each section, moreover the percentage of completely filled sections was evaluated. At all levels, no significant differences in terms of PGFA, PSFA, PVA and percentage of completely filled canals between groups were obtained (P > 0.05). On the contrary, when the data were pooled, the mean PGFA in the SAF group was 95.8%, whereas it was 93.2% in the WaveOne group (P less than 0.05). The percentage of sections completely filled was 77.8% in the SAF group, and 52.8% in the WaveOne group (P less than 0.05). Overall, the use of the SAF system in oval canals allows to obtain a significantly greater complete filling than the use of the WaveOne system.