For realization and partial automation of the solution of tasks of the special technique of microstructural analysis the program module integrated into GIS was developed by authors. Researches were conducted on the basis of the ArcView 3.2 program of the ESRI Company, which includes the internal environment of development – theobject-oriented Avenue programming language. This programming language is rather simple and was used by authors for development of necessary functions of the program module in relation to the spatial analysis of microstructures.The represented module in total with basic functions and the GIS tools allows carrying out pasting of separate sections images of a petrographic thin section, their joining in one system of relative coordinates, marking of all microstructures in thin section, marking of microobjects on types, on age and genesis. Besides, in a program code algorithms of automatic calculation of geometrical parameters of microstructures are put, and also there is a possibility of identification of various systems and generations of microcracks and microstructures. On the basis of reconstruction of geometry of a network of microcracks the module allows to count filtration characteristics (spatial and directional porosity and permeability) of rocks in paleo- and modern conditions at various stages of deformation of geological bodies. Representation of results in the form of simple charts is realized (schedules, histograms), and possibility ofcreation of roses charts, which are extremely necessary in process of studying of cracks in rocks for geology,hydrogeology and geophysics is also developed.