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In the modern economic conditions, the rational planning of costs and the complex process optimization are essential requirements to all organizations. Knowledge of costs is needed to correctly assess the economic performance of an organization. Competent and timely correction of tariffs for the obligatory medical insurance and rationalization of the requested financing of the medical organization depends on this assessment. In the present study, we analyze various methods of personalized cost accounting: the ratio of costs to charges (RCC); relative value unit (RVU); time-driven activity-based costing (TDABC), and the possibility of their adaptation to the specific needs of medical organizations. The personalized cost accounting incorporated into a medical information system allows for controlling, planning and carrying out a close internal management of financial activity. This function helps decision-makers: control the use of funds for medical care provision; increase the efficiency of management decisions; justify the prices of paid medical services; define the deficit and surplus work units; analyze the treatment cost for each patient, considering the diagnosis, method of treatment, age and other classification signs, including the reference to specialized departments; reduce the unnecessary “paper” work load on the medical personnel; model the future needs of the organization in accordance with the planned changes in the hospitalization policy; optimize, control and plan the budget with regard to the established standards of financial expenses. Implementation of this approach is expected to increase the work efficiency in most medical organizations and the entire healthcare system.