The authors discuss the problems of methodology in modern theoretical pathology in the light of acceleration of scientific technological development. It is emphasized that theoretical pathology must become fundamental medical science advancing new ideas. Deviation from the principle of the unity of structure and function should not be allowed. This deviation stems from the attempts to substitute the methodology of cognition for separate methods of investigation. The necessity of using qualitative and quantitative methods of investigation in their interrelation is shown as it is impossible to divide a universal systemic method into separate qualitative and quantitative ones. It is noted that the theory of pathology must be founded not only on sequential analysis of the object of investigation but also on the adequate synthesis of components and their relations.