Zika virus (ZIKV) infection in pregnancy is associated with birth and developmental alterations in infants. In this study, clinical records of 47 infants whose mothers had Zika during pregnancy or clinical manifestations compatible with Zika were reviewed. A description of the infants’ anomalies was established, and a neurodevelopmental assessment was performed on 18 infants, using the Evaluation of Infant Development (EDI for its initialism in Spanish) and DDST-II (Denver Developmental Screening Test II) tests. From his sample, 74.5% of the infants evaluated had major anomalies and 51.9% had minor anomalies. The incidence of major anomalies, related to trimester of pregnancy, was 84.2% for the first trimester, 77.8% for the second trimester, and 37.5% in the third trimester. A similar trend was observed in the frequency of infants without anomalies and was less evident in the incidence of minor anomalies (p = 0.016). Through neurodevelopmental assessments, EDI identified 27.8% of infants as having normal development, while 55.5% of affected infants had developmental delay, and 16.7% were at risk for developmental delay. The DDSST-II showed that 77.7% infants had delay in the gross motor and language area, 88.8% in the fine-adaptative motor area, and 72.2% in the personal–social area. In this work, children of mothers with ZIKV infection during pregnancy may have major or minor anomalies regardless of the trimester of pregnancy in which the infection occurred. The neurodevelopmental assessment shows that ZIKV can cause a developmental delay in infants with the fine-adaptative motor area being the most affected.