Although the manifestations of Down syndrome (DS) are well known, certain major birth defects such as duodenal atresia and endocardial cushion defects are present in some infants but not others, suggesting the possible role of other genetic or environmental factors interacting with the trisomy genotype. To explore the possible role of maternal factors in the presence of major defects among DS infants, we examined data from an epidemiologic study of DS conducted in metropolitan Atlanta. Of 219 DS infants born between 1968 and 1980, 50 had recorded cardiac defects, 9 had selected gastrointestinal atresias and 4 had oral clefts. We evaluated the association of these defects with several maternal factors including age, race, first trimester cigarette smoking, alcohol use, and fever. We found that different maternal factors were associated with several defects: (1) mother's race with cardiac defects (40% in blacks vs. 17% in whites, P less than 0.01), (2) mother's age with oral clefts (6% for less than 25 years, 1% for 25-34, and 0% for greater than 34, P less than 0.05), and (3) maternal first trimester fever with gastrointestinal defects (15% in infants with history of fever and 3% in infants without a history of fever, P less than 0.01). We also observed an inverse relationship between maternal alcohol use and the presence of ventricular septal defect. These findings suggest that maternal risk factors may influence the clinical manifestations of DS. In addition to searching for a genetic basis for the DS phenotype, we suggest that the role of environmental factors and maternal exposures be specifically explored in clarifying the genesis of various birth defects in Down syndrome.