The article is to study the development of computer-aided design of X-ray microtomography—the device for investigating the structure and construction of three-dimensional images of organic and inorganic objects on the basis of shadow projections. This article provides basic information regarding CAD of X-ray microtomography and a scheme consisting of three levels. The article also shows basic relations of X-ray computed tomography, the generalized scheme of an X-ray microtomographic scanner. The methods of X-ray imaging of the spatial microstructure and morphometry of materials are described. The main characteristics of an X-ray microtomographic scanner, the X-ray source, X-ray optical elements and mechanical components of the positioning system are shown. The block scheme and software functional scheme for intelligent neural network system of analysis of the internal microstructure of objects are presented. The method of choice of design parameters of CAD of X-ray microtomography aims at improving the quality of design and reducing costs of it. It is supposed to reduce the design time and eliminate the growing number of engineers involved in development and construction of X-ray microtomographic scanners.