BACKGROUND: The causes of choanal atresia or stenosis (CA) are largely unknown. Infant thyroxine (T4) levels collected during newborn screening may be proxy measures for a risk factor present during the critical period of development. Therefore, we conducted a case-control study to examine the association between newborn T4 levels and CA. METHODS: Data for cases with CA and controls were obtained from the Texas Birth Defects Registry for the period of 2004 to 2007. Information on infant T4 levels at birth was obtained from the Texas Newborn Screening Program. Controls (n = 3570) were drawn from unaffected births in Texas for the same period and frequency matched to cases (n = 69) on year of birth, then linked to the newborn screening database. Logistic regression was used to evaluate the association between continuous and categorical infant T4 levels and nonsyndromic CA. RESULTS: After adjustment for gestational age and year of birth, infant T4 levels were inversely associated with CA (adjusted odds ratio [AOR], 0.85; 95% confidence interval [CI], 0.80–0.90). We observed a linear trend (p < 0.001) across quartiles of T4; compared to infants with low levels, AORs for CA were 0.50 (95% CI, 0.28–0.91), 0.39 (95% CI, 0.20–0.75), and 0.15 (95% CI, 0.06–0.40) for infants with medium-to-low, medium, and high levels, respectively. CONCLUSIONS: Our findings suggest a role of low thyroid hormone levels in the development of CA, or that low newborn T4 levels are potential proxy measures of a risk factor present during the critical period. Birth Defects Research (Part A), 2012. © 2012 Wiley Periodicals, Inc.