BackgroundDocumentation of congenital heart disease diagnosis is important for optimal patient care. ObjectivesWe investigated longitudinal documentation of congenital heart disease (CHD) diagnosis among children who received a prenatal diagnosis of congenital heart disease at an academic health system in the southeastern United States. MethodsPatients born at our hospital in 2014–2018 were included in a retrospective analysis if they had a prenatal diagnosis of congenital heart disease. Medical records after the birth admission were analyzed for the presence of documented congenital heart disease diagnosis using International Classification of Disease (ICD) codes and free-text notes. ResultsThirty-two children contributing 482 health system encounters met inclusion criteria.Fifty-eight encounters (12%) did not have documentation of CHD. Multivariable analysis determined that Black as compared to White (OR: 6.4; 95% CI: 1.5, 27.3) was associated with non-documentation of CHD diagnosis at a given encounter. Documentation in free-text notes only (vs. ICD codes) was more common for Hispanic and older patients, and for non-cardiology encounters compared to cardiology clinic visits. Complex vs. simple CHD was associated with increased likelihood of documentation via ICD codes. ConclusionDespite a shared electronic medical record, congenital heart disease diagnosis was not always recorded in encounters within the same health system after prenatal diagnosis of congenital heart disease. Future work should explore opportunities to improve the consistency of documenting congenital heart disease diagnosis, especially among older children and children transferring care across clinics or health systems.