Screening for critical congenital heart disease (CCHD) using pulse oximetry has been endorsed by the American Academy of Pediatrics and the American Heart Association. We sought to determine the incidence of undetected CCHD in Tennessee and the diagnostic gap of CCHD in Middle Tennessee prior to screening implementation. The Tennessee Initiative for Perinatal Quality Care (TIPQC) Undetected CCHD Registry is a quality improvement initiative established to identify neonates discharged from the nursery with undetected CCHD. The TIPQC database was queried and a simultaneous review of all neonates with CCHD in the Middle Tennessee region was performed to define the incidence and identify the pre-screen diagnostic gap of undetected CCHD at the time of hospital discharge. In 2011, of 79,462 live births in Tennessee, 12 newborns had undiagnosed CCHD (incidence 15 per 100,000; 95 % CI 9-26 per 100,000). Nine of 12 (75 %) had coarctation of the aorta (CoA). There were no deaths due to undiagnosed CCHD. In the Middle Tennessee region, 6 of 45 neonates with CCHD were missed, for a diagnostic gap of 13 % (95 % CI 6-26 %). Prior to implementation of CCHD screening using pulse oximetry, 12 Tennessee neonates with CCHD were missed by prenatal ultrasound and newborn examination. CoA was the most common lesion missed and is also the CCHD most likely to be missed despite addition of screening using pulse oximetry. Continued evaluation of the diagnostic gap with particular attention to missed diagnoses of CoA should accompany institution of CCHD screening programs.