To determine prevalence and incident cases of CNS anomalies and other congenital disorders among fetuses of pregnant women with a clinical history compatible with ZIKV infection in Bucaramanga, Colombia. 88 fetuses (one twin pair) were evaluated, as part of a larger prospective cohort study evaluating the neurodevelopment of Zika exposed fetuses and infants, with one to four level III transvaginal ultrasound scans using a pre-established protocol. Ultrasounds were performed by a team of maternal fetal specialists at three referral clinical centres, between May 1, 2016 and February 28, 2017 (NCT 02943304). The overall rate of CNS anomalies was 30/84 (35.7%) [4 infants < 20 weeks, non-survivors were excluded from the denominator]: Microcephaly <-2 SD 16/84 (19.0%), 7/16 (43.8%) <-3 SD; cerebral calcifications 13/84 (15.5%), 69% frontal, 61% temporal, 61% parietal, and 30% occipital; ventriculomegaly 10/84 (12.2%); neuronal migration disorders 9/84 (10.4%); corpus callosum agenesis 5/84 (5.9%) and corpus callosum dysgenesis 14/84 (16.5%); posterior fossa anomalies 6/84 (7.1%); and arthrogryposis 1/84 (1.1%). Additionally, 11/88 (12.5%) of studied fetuses had non-CNS anomalies (54% congenital heart anomalies). Intrauterine growth restriction (<p10) was observed in 6/88 (6.8%) of the cohort. We found a significantly higher rate of CNS anomalies in this prospective cohort of Zika symptomatic mothers than previously published in the literature. This may be explained by the level of expertise performing the ultrasounds and/or the standardised transvaginal technique used. The most common anomalies observed were: alterations in corpus callosum, microcephaly, and calcifications.