We assessed nonanthrax vaccination data quality in the Defense Medical Surveillance System (DMSS) during 1998-2004. We sampled servicemembers' medical charts at 28 Military Treatment Facilities and estimated the agreement between DMSS electronic and medical chart vaccination data, conditional on the data in the medical charts. Our analysis included 3831 individuals who received 39,305 nonanthrax vaccine doses. Yellow fever vaccine category had the highest conditional sensitivity for exact date match (83.4%; 95% CI = 80.1, 86.3); most vaccine categories' conditional sensitivities improved over time. Our study suggests DMSS vaccination data may be acceptable for post-marketing vaccine safety studies for certain vaccines and timeframes.