Background: While encephalitis may be caused by numerous infectious, immune and toxic processes, the etiology often remains unknown. Methods: We analyzed multiple cause-of-death mortality data during 1999-2008 for the USA, using the 10th revision of International Classification of Diseases codes for encephalitis, listed anywhere on the death record, including ‘specified' and ‘unspecified' encephalitis. Annual and average annual age-adjusted and age-specific death rates were calculated. Results: For 1999-2008, 12,526 encephalitis-associated deaths were reported with 68.5% as unspecified encephalitis. The average annual age-adjusted encephalitis-associated death rate was 4.3 per 1 million persons, 1.3 for specified and 2.9 for unspecified encephalitis. Annual encephalitis-associated death rates had a significant downward trend (p < 0.01). The most common specified encephalitis deaths were herpesviral encephalitis (36.7%), Toxoplasma meningoencephalitis (27.8%) and Listeria meningitis/meningoencephaltis (6.8%). HIV was colisted with 15.0% of encephalitis-associated deaths, 58.4% of these with a specified code. Conclusion: Encephalitis-associated death rates decreased during 1999-2008, and herpesvirus was the most commonly identified infectious agent associated with encephalitis deaths. The high proportion of unspecified encephalitis deaths highlights the continued challenge of laboratory confirmation for causes of encephalitis and the importance of monitoring trends to assess the impact of new diagnostics and guide potential interventions.