Adverse events following pandemic (H1N1) 2009 vaccines ("2009 H1N1 vaccines") in Taiwan were passively reported to the National Adverse Drug Reaction Reporting System. To evaluate the completeness of spontaneous reporting, cases of death, Guillain-Barré syndrome (GBS), convulsion, Bell's palsy, and idiopathic thrombocytopenic purpura (ITP) after 2009 H1N1 vaccination that occurred between November 1, 2009 and August 31, 2010 were selected from the National Adverse Drug Reaction Reporting System (NADRRS) database and an additionally constructed nationwide large-linked database (LLDB), and matched on a unique personal identifier, date of vaccination (within ±7 days), and date of diagnosis (within ±7 days). Overall, matches occurred between the two data sources included 21 for death, 5 for GBS, 19 for convulsion, 22 for Bell's palsy, and 5 for ITP. The Chapman capture-recapture estimated spontaneous reporting completeness within 0-42 days of vaccination was 4% for death, 71% for GBS, 3% for convulsion, 9% for Bell's palsy, and 15% for ITP. For the interval ≥43 days after vaccination, reporting completeness was 0.1% for death, 14% for GBS, 0.1% for convulsion, <0.1% for Bell's palsy, and 0% for ITP. The estimated-to-expected ratio for Bell's palsy in the interval 0-42 days after vaccination was 1.48 (95% CI 1.11-1.98). Reporting completeness was higher for GBS than other adverse events after 2009 H1N1 vaccination. Linking the NADRRS to existing data sources in a capture-recapture analysis can be considered as an alternative to enhance Taiwan's postlicensure safety assessment of other routine vaccines. Nevertheless, the possibility of an increased risk for Bell's palsy detected by capture-recapture analyses needs further evaluation by controlled studies.