The effect of hospital organizational affiliation on perinatal outcomes is unknown. Using the 2004 American Hospital Association Annual Survey and Healthcare Cost and Utilization Project State Inpatient Databases, the authors examined relationships among organizational affiliation, equipment and service availability and provision, and in-hospital mortality for 5,133 infants across five states born with very low and extremely low birth weight and congenital anomalies. In adjusted bivariate probit selection models, the authors found that government hospitals had significantly higher mortality rates than not-for-profit nonreligious hospitals. Mortality differences among other types of affiliation (Catholic, not-for-profit religious, not-for-profit nonreligious, and for-profit) were not statistically significant. This is encouraging as health care reform efforts call for providers at facilities with different institutional values to coordinate care across facilities. Although there are anecdotes of facility religious affiliation being related to health care decisions, the authors did not find evidence of these relationships in their data.