INTRODUCTION: Because of the relatively high expense of collecting primary data and limited resources, electronically available, population-based hospital discharge data have been increasingly used for disease surveillance by public health researchers. The objective of this study was to compare the New York State Congenital Malformations Registry (CMR) data, which relies on hospital reports, with the hospital discharge files to identify cases in the CMR that were missed in the hospital discharge data files. The ultimate goal was to evaluate whether hospital discharge data can serve as the sole source of case ascertainment for a population-based birth defects surveillance program. METHODS: CMR cases that were born to the New York State residents for the years 2000 to 2005 were selected and matched to the hospital discharge files from the New York Statewide Planning and Research Cooperative System (SPARCS) for the same birth year period. Since the SPARCS database does not contain patient's name, extensive database matching and manual review by staff members were performed using identifying variables such as the hospital's permanent facility identifier, child's date of birth and medical record number, and mother's medical record number and residential address. RESULTS: Out of 66 757 CMR cases selected for the study period, 62 118 cases (93.1%) were matched to SPARCS hospital discharge records with International Classification of Diseases, Ninth Revision (ICD-9) codes that were reportable to the CMR, 3 444 cases (5.2%) were matched to SPARCS records with ICD-9 codes that were not reportable to the CMR, and 1 195 cases (1.8%) were not matched. The percentage of cases with multiple congenital malformations was significantly higher (21.3%) for the matched cases that had reportable ICD-9 codes in SPARCS, compared with that for matched CMR cases that had no reportable ICD-9 codes in SPARCS (10.2%). CONCLUSION: The study found that 93% of CMR infants selected for the study were matched to hospital discharge records with at least one ICD-9 code that was reportable to the CMR; 87 percent had reportable ICD codes in SPARCS that were exactly matched to those in the CMR, that is, all the birth defect codes in SPARCS were matched to those in the CMR. Thus, about 7 percent of CMR children with birth defects would have been missed if only hospital discharge files were used to ascertain the birth defect cases, indicating that there are limitations to using hospital discharge files as the sole source of case ascertainment for population-based birth defects surveillance programs. Copyright © 2010 Wolters Kluwer Health | Lippincott Williams & Wilkins.