The aim of this study was to evaluate the quality of the canal fillings performed by thermoplastic technique (Herofill) and cold lateral condensation (CLC) techniques in oval shaped canals following self-adjusting file (SAF) preparation using radiological, stereological, and microscopic evaluation methods. Twelve pairs of oval-shaped root canals were prepared with SAF and filled using CLC (n = 12) or the Herofill system (n = 12). The quality of the root canal filling was evaluated by (i) scoring bidirectional storage phosphor plate images, (ii) stereological (volumetric) analysis of cone beam computerized tomography (CBCT) images, and (iii) microscopic analysis of the cross-sectioned area of the canal and gutta-percha via image analysis software. Chi-square test, t-test, and Mann-Whitney U-tests were used respectively (p < 0.05) for the aforementioned evaluations. 58.33% of the fillings (total n = 24) that were found to be sufficient in a bucco-lingual (BL) projection were considered insufficient in the mesio-distal (MD) projection according to radiological scoring. The difference in the findings between the two types of projections (BL and MD) was significant (p < 0.05). The results of the stereological evaluation of CBCT images and image analysis of cross-sections showed no statistically significant difference between the CLC and Herofill (p > 0.05). Herofill was not superior to cold lateral compaction. Stereology can be used to obtain unbiased information about the volume of root canal fillings. Both filling techniques failed to achieve the desirable goal of 0% empty volume in all of the cases and all evaluation systems confirmed this result. SCANNING 38:427-433, 2016. © 2015 Wiley Periodicals, Inc.