Mathematical models are constructed and used as a methodology of various functioning systems structure investigation and performance analysis. The main goal of mathematical model usage is to perform wholesome diagnostics and correct work resumption of investigated system. In the article topological modeling method has been investigated by giving fundamental basics and application spheres by examples. Authors propose model construction method with an example from medicine by creating multiple diseases (arterial hypertension, atherosclerosis and diabetes mellitus) evolution topological model with formal aspects. Developed modeling method and united diseases model can be used to prognosticate evolution of diseases, perform inspection of used therapies and provide information for optimal therapy complex selection.