Organizations as social and business systems are heavily influenced by the environment. The environment, as an external factor of the organization that acts unannounced, significantly determines the desired organizational form. While they have to adapt to the existing conditions from the organization's environment, internal factors are usually under the control of the organization. This paper presents the importance of the influence of internal factors on the formation of the organizational structure of the company. The notion of organization and organizational structure is also treated. In particular, the main internal factors of the organization that the organization can influence are listed and explained. The purpose and goal of the paper is to determine the general characteristics of internal factors, their influence and action as well as the mutual influence on each other. A special goal of this paper is to analyze and evaluate their impact on selected companies "Kraš" d.d. and “Kandit” d.o.o. and finally, to compare the influences of internal factors on the organizational structure of selected enterprises.