The study aimed to identify and analyze the nationwide Health Information Systems (SIS) operating in Brazil from 2010 to 2018 and to understand the management and support structure for Information Technology (IT) in these systems in the Ministry of Health. This was a descriptive study based on document analysis, seeking to consolidate the data on nationwide SIS based on selection criteria referenced on the concept of SIS. The documents yielded incomplete and mutually disparate data, evidencing different interpretations of the concepts of systems and health information systems in the Ministry of Health. The survey found 54 nationwide Health Information Systems functioning from 2010 to 2018 and collected information on seven decentralized IT centers in Ministry of Health departments, which work autonomously from the Brazilian Health Informatics Department (DATASUS). The analysis of the logics of their functioning identified four groups of SIS pertaining to the following: monitoring relevant events for public health, greater control and monitoring of health programs in the Ministry of Health, registration of physical and legal persons, and a "new generation" of SIS that are developed and maintained by the Federal Government but differ from its verticalized programmatic logic, focused on administrative rationalization and improving the quality of services provided by the SUS at the local and regional levels.