Aim To compare the sealing ability of the same root fillings when measured by a conventional fluid transport method that uses water or by a modified fluid transport method that uses a wetting fluid as tracer. Methodology The amount of fluid transport along the same root fillings (AH26, cold lateral compaction of gutta-percha) was measured in a cross-over design in fluid transport set-ups using either water or a wetting fluid as tracer. Results A Wilcoxon signed-rank test revealed a significant difference in the amount of fluid transport measured along the same root fillings by the two fluid transport methods (P = 0.013). The fluid transport method using wetting fluid detected a significantly higher percentage of root fillings with fluid transport (P = 0.021). Conclusions Fluid transport using a wetting fluid as a tracer was more sensitive in the assessment of sealing ability of root fillings than the conventional fluid transport method using water.