Background Administrative data permit analysis of large cohorts but rely on International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM), and International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) codes that may not reflect true congenital heart defects (CHDs). Methods and Results CHDs in 1497 cases with at least 1 encounter between January 1, 2010 and December 31, 2019 in 2 health care systems, identified by at least 1 of 87 ICD-9-CM/ICD-10-CM CHD codes were validated through medical record review for the presence of CHD and CHD native anatomy. Interobserver and intraobserver reliability averaged >95%. Positive predictive value (PPV) of ICD-9-CM/ICD-10-CM codes for CHD was 68.1% (1020/1497) overall, 94.6% (123/130) for cases identified in both health care systems, 95.8% (249/260) for severe codes, 52.6% (370/703) for shunt codes, 75.9% (243/320) for valve codes, 73.5% (119/162) for shunt and valve codes, and 75.0% (39/52) for "other CHD" (7 ICD-9-CM/ICD-10-CM codes). PPV for cases with >1 unique CHD code was 85.4% (503/589) versus 56.3% (498/884) for 1 CHD code. Of cases with secundum atrial septal defect ICD-9-CM/ICD-10-CM codes 745.5/Q21.1 in isolation, PPV was 30.9% (123/398). Patent foramen ovale was present in 66.2% (316/477) of false positives. True positives had younger mean age at first encounter with a CHD code than false positives (22.4 versus 26.3 years; P=0.0017). Conclusions CHD ICD-9-CM/ICD-10-CM codes have modest PPV and may not represent true CHD cases. PPV was improved by selecting certain features, but most true cases did not have these characteristics. The development of algorithms to improve accuracy may improve accuracy of electronic health records for CHD surveillance.