The article presents the stages of formation and development of system approach and system analysis as the methodological basis for the development of automated control systems in healthcare. Given the contribution of the most well-known industry experts in the development of this activity. The results of the analysis of the development of organizational support Informatization of healthcare of the country in recent fiftieth anniversary. Shows examples of effective and ineffective-products of decisions. Described the experience of theoretical and experimental substantiation of creation of regional medical information-analytical center.