In the present paper the approach utilizing X-ray computed microtomography (micro-CT) for evaluation of the manufacturing quality of 3D-printed scaffolds is proposed. The approach is based on matching and comparison the spatial image imported from the stereolithography (STL) files with the real geometry of the scaffold obtained by micro-CT scanning. Using the approach six photopolymer resin scaffolds with varying wall thickness (0.5, 0.7, 0.9, 1.1, 1.3, 1.5 mm) fabricated using digital light processing (DLP) were tested. The manufacturing artifacts were studied on the virtual two-dimensional slices of the internal structure of the scaffolds. A decrease of thickness deviations of the real geometry from the STL model for the scaffolds with increase of the thickness walls was observed and described.