Abstract The Zika virus (ZIKV) epidemic has become a public health emergency following its association with severe neurological complications. We aim to discuss how the Brazilian National Health Information Systems can help to assess the impact of the ZIKV epidemic on health outcomes potentially related to ZIKV. Health outcomes potentially related to ZIKV infection were described based on a literature review of published studies on ZIKV infection outcomes and on recent protocols developed and published by the Brazilian Ministry of Health for different stages of the life cycle. These outcomes were correlated with the International Classification of Diseases 10th Revision (ICD-10) classification system, as this is the diagnostic classification registered in the Health Information System. A suggested list of 50 clinical manifestations, dispersed into 4 ICD chapters, and their information sources was created to help monitor the ZIKV epidemics and trends. Correlation of these selected ICD-10 codes and the HIS, as well as, a review of the potentialities and limitations of health information systems were performed. The potential of the Health Information System and its underutilization by stakeholders and researchers have been a barrier in diagnosing and reporting ZIKV infection and its complications. The ZIKV outbreak is still a challenge for health practice and the Brazilian Health Information System.