A study was conducted in vitro to assess and compare the extent of apical leakage of four dyes by two commonly-used evaluation methods. For the study, 120 single-rooted extracted teeth were prepared by the step-back technique and obturated by lateral condensation with gutta-percha and Roth 801 sealer. After randomly allocating the roots into six groups, they were immediately immersed in dye for 72 h, using vacuum for 30 min at 40 degrees C. Teeth were immersed in Eosin, Methylene Blue, Black India Ink and Procion Brilliant Blue and cross-sectioned in 0.7 mm thick slices. Those immersed in Black India Ink and Procion Brilliant Blue were also evaluated by the clearing process. Dye penetration was assessed using a stereomicroscope. A statistically significant greater dye penetration was measured in the cross-sectioned group compared to the clearing group using the same dyes (Black India Ink, P = 0.020, Procion Brilliant Blue, P = 0.040). In the cross-section groups, no statistical significant difference was observed in the amount of leakage comparing the four dyes. No statistically significant difference was found in the leakage pattern of Procion Brilliant Blue and Black India Ink using the clearing technique (P = 0.797). The evaluating method (cross-sections versus clearing) rather than the dye properties was the main difference between results. More research is needed to standardize dye leakage studies.