Background and Objective: Socioeconomic markers are associated with a higher risk of arbovirus infections such as dengue, Zika and Chikungunya. However, research on the relationship between socioeconomic factors and congenital Zika syndrome (CZS) remains scarce. In this study we investigated the relationship between socioeconomic markers and CZS in Brazil. Methods: We conducted a cross-sectional population-based study including all registered live births in Brazil (Live Births Information System) from 1 January 2015 to 31 December 2018. To assess CZS status, we linked the live births system with the Public Health Event Record. We used logistic regression models to estimate the OR and 95% CIs of CZS. Results: We included 11,366686 live births, of which 3,353 had CZS. Live births of mothers who self-identified as black or mixed race/brown were 1.72 (95% CI 1.47 to 2.01) and 1.37 (95% CI 1.24 to 1.51)) more likely to have CZS. Live births from single women compared with married women and those from women with less than 12 years of education compared with those with more than 12 years of education also had higher odds of CZS. In addition, those with fewer prenatal care appointments had increased odds of CZS in the nationwide data. However, in the analyses conducted in the Northeast region (where the microcephaly epidemic started before the link with Zika virus was established and before preventive measures were known or disseminated), no statistical association was found between the number of prenatal care appointments and the odds of CZS. Conclusions: This study shows that live births of the most socially vulnerable women in Brazil had the greatest odds of CZS. This disproportionate distribution of risk places an even greater burden on already socioeconomically disadvantaged groups, and the lifelong disabilities caused by this syndrome may reinforce existing social and health inequalities.