Objectives. To identify the barriers to the quality of information in health facilities in the Amazon region, exploring the case of three health information systems: the epidemiological vigilance, the daily recording of service, and the registry of deaths linked to HIV/AIDS, hepatitis B, and congenital syphilis. Materials and Methods. A quali-quantitative methodology was applied. On the one hand, 57 semi-structured interviews were conducted with administrative and assistance staff at health facilities; on the other hand, a survey was applied. One hundred and twenty health facilities in the regions of Amazonas, Huánuco, Loreto, Madre de Dios, San Martín, and Ucayali. Results. Eight barriers were identified, which were linked mainly to the human resource, to sociocultural aspects, and weaknesses of the health system. Conclusions. The barriers identified for the quality of the information in the selected information systems in health facilities in the Amazon region reflect a multidimensional problem, so strategies for improvement in the subject should be considered.