Neural tube defects (NTDs) are among the most common of birth defects. Despite the many gene candidates identified in certain population; none have thus far been regarded as compelling enough as a candidate for different populations. As candidate genes for NTDs, this study focussed on Ephs and ephrins owing to growing evidence for the role of this gene family during neural tube closure in mouse models. Eph and ephrin genes were analysed in 31 Malaysian individuals comprising 7 individuals with sporadic spina bifida, 14 parents and siblings and 10 unrelated controls. Whole exome sequencing analysis was performed to identify variants in 22 known EphAs, EphBs, ephrinAs and ephrinBs genes. All candidate variants in Eph-ephrin genes were subjected to bioinformatics analysis to determine possible pathogenicity. We reported 3 out of 7 spina bifida probands and 3 out of 13 parents and 1 twin-sibling, carried a variant in either EPHA2 (rs147977279), EPHB6 (rs780569137) or EFNB1 (rs772228172). Analysis of public databases like 1000 Genome phase 3, GnomAD, ExAC, ESP, TOPMED and SGVP shows that these variants are rare, and they were not present in any of the unrelated controls. In exome datasets of the probands and parent of the probands with Eph and ephrin variants, the genotypes of spina bifida-related genes were compared to investigate the probability of the gene-gene interaction in relation to environmental risk factors. In summary, we report the presence of Eph and ephrin gene variants that are prevalent in a small cohort of spina bifida patients in Malaysian families.