Invasive meningococcal disease (IMD) completeness of reporting has never been assessed in New York City (NYC). We conducted a capture–recapture study to assess completeness of reporting, comparing IMD reports made to the NYC Department of Health and Mental Hygiene (DOHMH) and records identified in the New York State hospital discharge database [Statewide Planning and Research Cooperative System (SPARCS)] by ICD-9 codes from 1989 to 2010. Reporting completeness estimates were calculated for the entire study period, and stratified by year, age group, clinical syndrome, and reporting system. A chart review of hospital medical records from 2008 to 2010 was conducted to validate hospital coding and to adjust completeness estimates. Overall, 2194 unique patients were identified from DOHMH (n = 1300) and SPARCS (n = 1525); 631 (29%) were present in both. Completeness of IMD reporting was 41% [95% confidence interval (CI) 40–43]. Differences in completeness were found by age, clinical syndrome, and reporting system. The chart review found 33% of hospital records from 2008 to 2010 had no documentation of IMD. Removal of those records improved completeness of reporting to 51% (95% CI 49–53). Our data showed a low concordance between what is reported to DOHMH and what is coded by hospitals as IMD. Additional guidance to clinicians on IMD reporting criteria may improve completeness of IMD reporting.