The subject matter and the purpose of this paper is to present the business organization of the banking system in the Republic of Croatia. In order to demonstrate the business organization of the banking system, secondary data collection methodology has been used. I.e. this is the data collected from Internet sources, professional literature for educational institutions of economic orientation and books closely related to the topic of this paper. In addition, description method has been used by which it is introduced to the concepts and types of business organizations and the banking system operations. In the introductory part of the paper it is present the topics that will be examined in detail later in the paper. The main part of the paper closely examines the basic concepts of banks, business organizations, types and division of business organizational structure, and factors affecting the business organizational structure and provides examples of organizational structures of the banks in the Republic of Croatia. Two commercial banks have been selected for comparison of their organizational structures and Croatian National Bank. The conclusion provides an overview of the theme of this paper as a whole, which is based on observation and study of the organizational structure of the banking system in the Republic of Croatia. In the end of this paper gives a list of references, charts and images used in this paper.