BACKGROUND & OBJECTIVES: : Accurate identification of major malformation cases from administrative databases is crucial for perinatal epidemiology. In Quebec, most of major malformations are detected in hospital, however administrative databases capture diagnoses data from both hospitals and other medical facilities. We aimed to compare the prevalence of major congenital malformations identified from administrative databases diagnostic codes (ICD-9 and ICD-10) with 2 definitions: diagnoses made in hospital only vs. diagnoses made in hospital and other medical facilities. We further evaluated the impact of using each definition to quantify the association between maternal use of asthma controller medications and the prevalence of major malformations at birth and during the first year of life. METHODS: A cohort of pregnancies from asthmatic women between 1990 and 2010 was formed through the linkage of administrative databases from Quebec. We calculated the prevalence of major malformations identified in the 1^st year of life of the newborn using the 2 case definitions. We also calculated the crude odds ratio (OR) of major malformations associated with maternal use of inhaled corticosteroids (ICS) and long-acting beta-agonists (LABA) in the 1^st trimester of pregnancy. RESULTS: From 30655 pregnancies, 2090 (6.8%) major malformations were identified with hospital diagnostic codes only vs. 2748 (9.0%) with hospital and other medical facilities diagnostic codes. The OR of major malformations associated with ICS was 1.1 (95%CI: 1.0-1.2) with the first and 1.1 (95%CI: 1.0-1.2) with the second case definition. Corresponding results were 1.3 (95%CI: 1.0-1.6) and 1.1 (95%CI: 0.9-1.4) for LABA exposure. CONCLUSIONS: The case definition of congenital malformations had a considerable impact on the prevalence of major congenital malformations, but less impact on the associations we examined. The percentage of false positive cases when using all medical facilities diagnostic codes in the case definition is unknown and should be the objective for future research.