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Choanal atresia is a well-defined congenital malformation; however, little is known about its prevalence and risk factors. Data from the Iowa Registry for Congenital and Inherited Disorders were used to examine prevalence, infant, and maternal characteristics of choanal artesia. Data from the National Birth Defects Prevention Study (NBDPS) were used to examine selected risk factors for choanal atresia. Overall prevalence was estimated as number of choanal atresia cases per 10,000 live births with 95% confidence intervals (CI)s. Crude and adjusted odds ratios (OR)s and 95% CIs were estimated to investigate selected risk factors. The overall prevalence of choanal atresia among live born deliveries in Iowa from January, 1998 through December, 2005 was 0.46 (95% CI=0.27, 0.78) per 10,000 live births. Using data from the NBDPS, choanal atresia cases were compared to unaffected control infants for births from October 1997 through December 2005. Overall, case infants compared to control infants were more likely to be female, preterm, and a multiple birth. For all choanal atresia cases combined, odds of high maternal zinc (OR=2.1; 95% CI=1.2, 3.9) and vitamin B-12 (OR=2.4; 95% CI=1.4, 4.3) intake in the year prior to pregnancy, and maternal periconceptional (one month before through three months after conception) exposure to anti-infective urinary tract medications (OR=3.3; 95% CI=1.3, 8.4) were significantly elevated among case compared to control mothers. For isolated choanal atresia cases (those with no additional major malformations), odds of maternal periconceptional exposure to passive cigarette smoke (OR=2.3; 95% CI=1.0, 5.3) as well as maternal intake of 3 or more cups of coffee per day one-year prior to pregnancy were increased (OR=2.9; 95% CI=1.3, 6.4) for case compared to control mothers. The reverse was found for low maternal intake of pantothenic acid (OR=0.4; 95% CI=0.2,0.9) and vitamin A (OR=0.3; 95% CI=0.1, 0.8) one-year prior to pregnancy. The current study provided support for potential associations between maternal health behaviors before and during pregnancy and choanal atresia; however, the findings were based on a modest number of cases. The study needs to be replicated in a larger case sample, also examining the role of genetics in choanal atresia.