The business architecture, whose integral part is an organizational and management company structure, will be playing more important role in the future while pursuing its business goals. As a matter of fact, the organization and management of business processes that constitute its organizational and management structure demonstrate significant changes as a result of the changeable business environment. These issues are discussed in this article. The testing data set 381 SMEs (from which 114 were micro-enterprises, 141 small-scaled enterprises and 126 mid-scale enterprises, including without limitations enterprises from South Bohemian Region) analyzed applied organizational and management structures in separate scale categories of enterprises including degrees and stages of management. Pearson’s chi-squared test was used as a statistical method; pvalue was employed to test zero and alternative hypotheses. SMEs manifested a transition from linear and line-staff structures to matrix and functional ones; mid-scale enterprises used strategic business units. Microenterprises and partly small-scale enterprises employed degree of management, mid-scale 3 and more degrees of management. The conclusion of the article specifies the estimated development of the organizational architecture in SMEs in the Czech Republic in relation to expected changes in the external business environment in particular.