Purpose: To compare scanning electron microscopic (SEM) and confocal laser scanning microscopic analyses (CLSM) of hybrid layer thickness and the number of dentinal tubules penetrated with composite resin inside the root canal on identical samples. Materials and Methods: Central maxillary incisors were restored using fiber posts (FRC Postec) inserted with a chemically curing composite resin (Clearfil Core/New Bond). Two different fluorescent dyes were used to respectively label adhesive and composite resin. Each root was sectioned into two slices starting 2 mm below the cementoenamel junction. SEM (low vacuum mode) and CLSM (dual fluorescence mode) analyses of 18 samples were performed. Hybrid layer thickness was measured at five characteristic points of each sample and the number of dentinal tubules penetrated with composite resin was counted on both corresponding images by two independent observers. Correlation coefficients as well as pairwise comparisons were calculated for both parameters. Results: SEM and CLSM measurements of hybrid layer thickness were positively correlated (r2 = 0.772; Pearson), and thickness was significantly higher after evaluation with CLSM (p 0.0005; Wilcoxon). The observed number of dentinal tubules penetrated with composite resin revealed a nonsignificant correlation (r2 = 0.111; p = 0.193). Significantly lower tag numbers were counted when using SEM (p = 0.010; Wilcoxon). Conclusion: With respect to the variability of the hybrid layer measurements, the two methods yielded comparable results. CLSM provided more detailed information regarding the penetration and distribution of resin cement and adhesive than did SEM imaging. Keywords: scanning electron microscopy, confocal laser scanning microscopy, correlation, hybrid layer, root canal dentin