Background This study compared natural root caries lesions with artificial root caries lesions prepared with one of the two demineralising solutions. Methods Twelve natural root caries lesions on upper incisors and 24 artificial root lesions were prepared on sound root surfaces using 50 mM acetic acid, 1.5 mM CaCl2, 0.9 mM KH2PO4 at pH 5.0 or 80 mL/L Noverite K‐702 polyacrylate solution, 500 mg/L hydroxyapatite, 0.1 mol/L lactic acid at pH 4.8 (n = 12/group) for 96 hours. Lesions were scanned using micro‐CT. Inciso‐gingival oriented images were analysed and mineral density calculated at 7.5 μm increments from the surface to 225‐μm deep. Sectioned lesions were analysed by Knoop microhardness up to 250 μm from the lesion surface. Data were analysed by the Dunn's test with Bonferroni correction. Results Natural and artificial lesion mean mineral densities were not statistically different (P > 0.05). Mineral density from the surface to 75 μm was greater in natural lesions and from 150 to 225 μm was greater in artificial lesions (P < 0.05). Microhardness values were statistically higher in artificial lesions (P < 0.05); no difference was found among artificial lesions produced by the two solutions (P > 0.05). Mineral density and microhardness of natural and artificial root caries are different from each other. A greater mineralized surface layer existed on natural lesions.