OEIS is the acronym of a malformations complex association including omphalocele, exstrophy of bladder or cloaca, imperforate anus, and spinal defects. It has a very low prevalence, ranging from 1/82,000 to 1/200,000 live births (LB). The etiology of OEIS is unknown. Virtually all cases are sporadic, and specific associated risk factors uncertain.ObjectivesThis study aimed to determine the prevalence, clinical spectrum, possible early pregnancy exposures, and demographic characteristics as potentially associated risk factors in a sample of Mexican cases.MethodsWe conducted a multihospital based case–control study on 12 cases with the OEIS complex identified in 1,195,020 LB born from January 1978 to December 2015. All comparisons performed were matching 1:3 the relation of cases and controls, respectively, considering the p‐value of ≤.05 as statistically significant.ResultsThe prevalence of OEIS was 1.004/100,000 (1/99,585) LB. The frequency of bladder/cloacal exstrophy was 75 and 25%, respectively, omphalocele was 83.3%, and imperforate anus and spinal defects, 75.0% each. Two pairs of twins discordant for the defect exhibited the severest OEIS phenotype. Except for the higher frequency of maternal first pregnancy trimester influenza infection, early perinatal mortality and a twining trend association, none other variable differed significantly.DiscussionThe prevalence of OEIS in our sample is within the highest reported worldwide. First‐trimester pregnancy maternal influenza infection and twining emerge as associated risk factors for OEIS. Although twin zygosity was not defined, the observed severest phenotypes in twins endorse the hypothesis that OEIS and monozygotic twinning are features of disturbances on early blastogenesis.