Authors state methodological bases of construction of automated control system (ACS) of the medical service of the Armed Forces and the Navy. A basis of the methodological rules is made by the analysis of conformity of the purpose (preservation and strengthening of the servicemen' health and management composed process: the tax, processing, storage and distribution of data and preparation of the decision, i.e. the information-and-target approach. The automation of processes of profile activity of forces and means of the medical service provides the constant control by functioning of medical units and institutions. The main targets of the ACS' functioning are processing of the information about quality of rendering of the medical care to the servicemen, its timeliness and profitability, productivity of their labour, conformity of work results to the medical standards and others. The quality and the efficiency of ACS'application is defined by a level of information maintenance. ACS of the medical service should be subsystem of the automated control system of the troops.