Tooth-erosion is the surface loss of dental hard tissue mostly associated with an acid attack. The aim was to compare dentin and enamel erosion depth measurements using micro-computed tomography (microCT) and light microscopy (LM). Enamel/dentin blocks were prepared from caries-free human molar-teeth (N = 12). Teeth were sectioned to a rectangular shape of 4 × 4 × 6 mm. Specimens were treated with water (NC) or 1.0% citric-acid solution (PC). After treatment, specimens were scanned with micro-computed tomography. On completion, specimens were sectioned and observed under a light-microscope. Lesion depth was observed with 10× magnification and images transferred to Simpleware software. Vertical distance from lesion surface to bottom was measured. Pearson correlation test was used to evaluate correlation and Wilcoxon Signed Rank test to evaluate differences in the two-analysis methods. Mean enamel erosion depth was 0.63 and 38.38 μm (microCT) and 0.54 and 39.43 μm (LM) for NC and PC, respectively. Dentin erosion depth was 0.72 and 48.05 μm (microCT) and 0.56 and 49.92 μm (LM) for NC and PC, respectively. There was a significant correlation between the two-analysis methods (r = 0.998; p <.001). No statistically significant difference in results were obtained when microCT and LM were compared (p =.584). This results obtained from the current study suggested that erosion depth measurements made using microCT and LM yielded comparable results. The microCT method is preferred if the conservation of specimens is desired.