The California Encephalitis Project was initiated in June 1998 to identify the causes and characterize the clinical and epidemiologic features of encephalitis in California. Testing for >or=13 agents, including herpesviruses, enteroviruses, arboviruses, Bartonella species, Chlamydia species, and Mycoplasma pneumoniae, was performed at the Viral and Rickettsial Disease Laboratory (Richmond, California). Epidemiologic and clinical information collected for each case guided further testing. From June 1998 through December 2000, 334 patients who met our case definition of encephalitis were enrolled. A confirmed or probable viral agent of encephalitis was found in 31 cases (9%), a bacterial agent was found in 9 cases (3%), and a parasitic agent was found in 2 cases (1%). A possible etiology was identified in 41 cases (12%). A noninfectious etiology was identified in 32 cases (10%), and a nonencephalitis infection was identified in 11 (3%). Despite extensive testing and evaluation, the etiology of 208 cases (62%) remained unexplained.