There appears to be an increased frequency of cystic fibrosis (CF) among infants with jejunoileal atresia (JIA). However, the figures vary widely, and no population-based data exist. The purpose of this study was to quantitate the magnitude of the association between JIA and CF in Atlanta using population-based data from 1968 to 1995. Case subjects included all infants with isolated JIA born during 1968-1995 to mothers residing in the five-county metropolitan Atlanta area at the time of birth. To ascertain cases, we reviewed records of the Metropolitan Atlanta Congenital Defects Program (MACDP), a population-based birth defects registry. Caucasian JIA cases were cross-referenced with patients in the CF registry at the Egleston Cystic Fibrosis Center at Emory University to more completely ascertain the diagnosis of CF among JIA cases. During 1968-1995, MACDP ascertained a total of 94 isolated JIA cases, for a birth prevalence of 1.8/10,000 live births. Among the cases, 38 were Caucasian, 52 were African-American, and 4 were of Asian or Hispanic ethnicity. Four of the 38 Caucasian JIA cases (11%) also had CF. The expected number of JIA cases with CF is 0.019 based on the estimated population incidence of 1/ 2,000 for CF. The observed to expected (O/E) ratio of Caucasian JIA cases with CF is greater than 210 (P<0.0001). Caucasian infants with JIA have more than 210 times the risk for CF compared with Caucasian infants in the general population. The results of this study have implications for the management of infants born with JIA and genetic counseling for families with affected infants.