Introduction:The use of secondary data for health service research has been increasingly common, having the advantage of acquiring information faster and cheaper, in addition to its larger population, temporal and geographical amplitude. Objectives: The aim of this study was to describe problems in the quality of information about hospitals characteristics and hospitalizations in Brazil. Methods: The National Database on Health Units (CNES), the Public Hospital Information System (SIH), and the Private Hospital Information System (CIH) were analyzed. We explored "coverage," "completeness," "consistency," and "validity" as quality dimensions. Results: There are complete and consistent basic registration data for hospitals, and most of them sent some information about the production of hospitalization. CIH covered 55% of admissions, and SIH exceeded 100%. The inadequate filling of the "procedure," "main," and "secondary diagnosis" fields is higher than expected, especially for CIH. Conclusion: Improvements in databases are required to qualify the analysis and increase its potential use, contributing with strategic studies that support decision-making in the planning of hospitals and health care networks.