Objectives: Conventionally, 'gold standards' used in the evaluation of different caries diagnosis techniques are based on histological sectioning. Such a procedure, however, requires cumbersome sample preparation, and induces tissue loss and irreversible sample destruction. Micro Computed Tomograhy (micro-CT) allows nondestructive imaging of the internal tooth structure, with information being visualized either as discrete sections or as 3D volume renderings.Methods: Micro-CT images were compared to clinical and histological evaluations of 16 extracted teeth, encompassing different pathologies. Clinical evaluation was performed by a panel of three dentists and three graduate students on models containing 3 teeth, among which the central one was previously evaluated by micro-CT. Caries was rated using 6 graduations (sound, probably sound, white/brown spot, enamel caries, dentine caries limited to half of dentin depth, deep dentine caries). Micro-CT scans were acquired using a desktop system (SkyScan-1072, Belgium), based on a combination of X-ray projection microscopy and tomographic data reconstruction. In this system, an air-cooled X-ray point source (20-130 kV / 300 µA, focal spot size \textasciitilde{}8 mm) illuminates the object with a divergent beam, and magnified shadow pictures are detected by a 2D X-ray CCD camera (512 x 512 pixels). Cross-sectional images were reconstructed at a spatial resolution of 14µm3, using a Feldkamp cone-beam algorithm. Histological evaluation was performed using a Leitz hard tissue microtome (600 µm sections) and a stereomicroscope. Spearman{\textquoteright}s rank correlation analysis was performed between the histological, micro-CT, and clinical outcomes.Results: The micro-CT analysis demonstrated good agreement with histological measurements (r = 0.89, p < 0.001), whilst the clinical evaluations were found to be much less correlated with the micro-CT analysis (r = 0.39, p < 0.001) and histological data (r = 0.42, p < 0.001).Conclusion: Micro-CT imaging was shown to provide an interesting alternative to histological sectioning in the evaluation of caries diagnosis. As a nondestructive technique, micro-CT allows longitudinal evaluation of the same tooth material.