We conducted a case-control study of maternal sex hormone exposure and the risk for major malformations. Using population-based surveillance data from the Metropolitan Atlanta Congenital Defects Program, we analyzed interviews from 1970-1979 for first trimester exposures to sex hormones among mothers of children with the following defects: oro-facial clefts; Down syndrome; diaphragmatic hernia; limb reduction defects; and esophageal, intestinal, or anal atresia. During the study period, 1,396 children with at least one of these defects were born in the surveillance area and 79% of the mothers were interviewed. For each defect category, the other defect categories served as the comparison group. We found no associations between any defect and oral contraceptive exposures; however, we did find an association between esophageal atresia and sex hormone exposure (odds ratio (OR) = 2.8, p = 0.009). Sex hormone exposures were subdivided, and associations persisted between esophageal atresia and 1) progestins and non specified sex hormones combined, and 2) hormonal pregnancy tests. Our findings suggest a relationship between esophageal atresia and non contraceptive sex hormone exposures. If causal, however, exposure would have a low absolute risk, on the order of 6/10,000 exposed live births.