To describe and analyze the changes in anthropometric parameters in children with congenital Zika syndrome (CZS) from birth to four years of age. This prospective study evaluated 117 children diagnosed with CZS. Anthropometric indices evaluated annually were classified with respect to presence of microcephaly and adequacy of weight-for-age, length/height for-age and body mass index-for-age (BMI-for-age). At birth, 69.6% of the children had microcephaly, 90.2% had adequate weight and 72.1% had adequate length. The following year, an increase occurred in the proportion of children with microcephaly, with a reduction of those with adequate weight. In the second year, the proportion of children with microcephaly increased again, while those with adequate BMI decreased. In the third to fourth years of life, a reduction was found in the proportion of children with adequate height. Anthropometric indices are affected in children with CZS over the first four years of life and appear to be potentiated over time.