The ZIC genes comprise a family of transcriptional factors associated with neural tube defects (NTDs) in mice and with holoprosencephaly in humans. An allelic variant of ZIC2, a CAC repeat within the first exon, was reported in association with an increased risk of non-syndromic NTDs in patients with a Hispanic ethnic background. We investigated whether this 10-residue histidine tract polymorphism of the ZIC2 gene (c.718_720dupCAC) was associated with the risk of NTDs in a sample of 138 patients and their parents from the Latin American Collaborative Study of Congenital Malformations (ECLAMC) hospital network. Analysis with log-linear models of 138 family triads of mother, father and affected child did not provide evidence to support the notion that case (or maternal) 10H/10H or -/10H genotypes were associated with NTDs in this South American population sample, where the 10H variant occurred in 5% of newborns affected with NTDs. We also described the first example of the homozygous state of the 10H allele in a patient with cephalocele, holoprosencephaly and microphthalmia, but did not ascertain whether this polymorphism is associated with the increased risk of a specific subgroup of NTDs, as a normal father of a patient with anencephaly presented the same genotype.