OBJECTIVE: To measure the degree of integration of the Electronic Citizen’s Record (PEC - Prontuário Eletrônico do Cidadão) of the e-SUS Primary Care Strategy (e-SUS AB - Estratégia e-SUS Atenção Básica) in the view of other Brazilian´s National Health Information Systems (SNIS - Sistemas Nacionais de Informação em Saúde), relating to the internal political-organizational structure of the Brazilian Ministry of Health (MH). METHODS: This is a qualitative case study. Data collection was carried out through document analysis and semi-structured interviews. In the first stage, we sought to clarify how many SNIS were in use in the Primary Care (PC) of the Unified Health System between 2013 and 2017. Then, we defined as criterion the maintenance of data collection interfaces by the Ministry of Health even after the implementation of the PEC/e-SUS Primary Care in order to measure the integration. RESULTS: 31 SNIS were identified in Primary Care. We observed that 12 of them were completely integrated and 15 presented no unification of interfaces related to PEC/e-SUS Primary Care. Another 4 have partial integration. By correlating these data with the political-organizational structure of the MS, we observed a greater integration with the systems managed by the Department of Primary Care and a persisted fragmentation in SNIS, especially those under the management of the Health Surveillance Department (Secretaria de Vigilância em Saúde). The disparity between the integration of the PEC/e-SUS Primary Care with the Health Surveillance SNIS is a sign of the persistence of the division and the false dichotomy between Health Care and Health Surveillance practices and processes in the Ministry of Health – even 30 years after the foundation of the SUS and unification of the state structures of social security hospital care and federal public health in MH. CONCLUSION: Although still insufficient, the systems integration carried out by the e-SUS Primary Care Strategy, which focuses on reducing user interfaces, can be considered a new fact on the SUS information and information policy agenda.