Modern business of health institution means the use of modern medical information system (MIS). The modern MIS must to enable the detailed monitoring of medications consumed. In order to obtain a realistic picture of consumed medications and medications in a warehouse of healthcare facilities, it is necessary to develop a special module for the management of medications and integrated the same with the module for invoicing services within the MIS. This paper shows software module for the management of medications as well as its integration with MIS MEDIS.NET. This paper shows the ability to generate dynamic reports via business intelligence tools Pentaho in order to detailed monitoring of expenditure of medications and adequate reporting management of health institutions on the basis of data collected using the module of management of medications and invoicing modules for delivery of health services.