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BACKGROUND—The etiopathogenesis of microtia is still unknown in the majority of the cases, particularly for individuals presenting with isolated microtia. Our aim was to evaluate potential risk factors for this condition using a case-control approach. METHODS—We analyzed data from 1,194 livebirths with isolated microtia enrolled in the ECLAMC study (Estudio Colaborativo Latino Americano de Malformaciones Congenitas) from 1982 to 2011 and their respective controls. Odds ratios were estimated with conditional logistic regression models along with 95% confidence intervals for the resulting odds ratio estimates controlling for the effects of potential confounders (sex, maternal age, hospital and year of birth) for an adjusted OR (aOR). RESULTS—Multiparity was associated with a higher risk of microtia compared to primiparity (aOR 1.5, 95%CI 1.2–1.8), with women who had eight or more prior pregnancies having the highest risk (aOR 2.8, 95%CI 1.6–5.2). Women who presented with cold-like symptoms were at higher risk for microtia (aOR 2.2, 95%CI 1.2–3.9) as well as those that used tobacco or alcohol during pregnancy (aOR 1.7, 95%CI 1.1–2.5 and aOR 1.4, 95%CI 0.9–2.1, respectively). The association with alcohol use appeared to be limited to those women who reported binge drinking during pregnancy (aOR 1.4, 95% 0.7–2.9). Cases from hospitals at low altitude (< 2,500 m) tended to have more severe types of microtia than those from hospitals at high altitude. CONCLUSIONS—These results support the hypothesis that in addition to teratogens other nongenetic risk factors contribute to the occurrence of isolated microtia.