We compared perinatal information submitted to the Canadian Institute for Health Information (CIHI) hospitalization database with information submitted to the Nova Scotia Atlee Perinatal Database (NSAPD) in order to assess the accuracy of the CIHI data. Procedures such as Caesarean delivery were coded accurately (i.e. sensitivity of 99.8%; specificity of 98.7%). Postpartum hemorrhage, induction of labour and severe intraventricular hemorrhage also had sensitivity and specificity rates above 85% and 95%, respectively. Some diagnoses, defined differently in the two databases, were less accurately coded, e.g. respiratory distress syndrome (RDS) had a sensitivity of 50.9% and a specificity of 99.8%. Restriction to more severe forms of the disease improved accuracy, e.g. restriction of RDS to severe RDS in the NSAPD and identification of severe RDS in the CIHI database, using codes for RDS and intubation, resulted in a sensitivity of 100% and a specificity of 99.6%. Our study supports the use of CIHI data for national surveillance of perinatal morbidity, with the caveat that an understanding of clinical practice and sensitivity analyses to identify robust findings be used to facilitate inference.