This article describes the Salvador Primary Care Longitudinal Study of Child Development (CohortDICa). The exposed group was defined by confirmation of Congenital Zika Syndrome (CZS) diagnosed through computed tomography, magnetic resonance or transfontanellar ultrasound. A random selection of the 169 exposed children led to a subgroup of 120 children who were paired with children from the Live Birth Information System, according to birthdate, residence in the same street or neighborhood, and gestational age, resulting in 115 subjects in the non-exposed group. Following recruitment and before the participants completed 42 months, three measures were applied to assess cognitive, motor, and language performance, corresponding to three home visits. Social characteristics of the families and children, and the neurocognitive development of the children will be compared across the CZS exposed group (n = 147), the typical children with no exposure to CZS (n = 115) and the STORCH exposed group (Syphilis, Toxoplasma gondii, Rubella, Cytomegalovirus, and Herpes simplex) (n = 20). Primary Health Care (PHC) should include long-term care strategies for the care of children and family members, and might benefit from the research, teaching, and extension activities provided in this study. In the face of the consequences of the Zika virus epidemic, an opportunity arose to intervene in the integrated care of child development within PHC, including, on an equal basis, typical children and those with delays or disabilities in the first six years of life.