The first confirmed cases of West Nile virus (WNV) in the Western Hemisphere were reported in the state of New York in 1999. Since then, the virus has spread throughout the eastern and central United States and continues to extend westward. This report describes clinical signs and microscopic lesions associated with WNV infection in a Suffolk ewe and an alpaca, 2 species in which the disease has not been reported previously. In late August 2002, a 4.5-year-old female alpaca developed an acute onset of clinical signs characterized by torticollis, hyperesthesia, ataxia, recumbency, and altered mentation. The animal died 3.5 days after the onset of clinical signs. Microscopic examination of the brain revealed a mild to moderate, diffuse, lymphoplasmacytic meningoencephalitis. In early September 2002, a 3-year-old Suffolk ewe developed a rapidly progressive illness characterized by ataxia and convulsions. The apparent duration from onset of clinical signs until death was less than 8 hours. The ewe had a moderate, diffuse, lymphoplasmacytic meningoencephalitis with focal gliosis. Reverse transcription-polymerase chain reaction assays and immunohistochemistry on the brain were positive for WNV in both animals. These cases demonstrate that WNV is capable of causing sporadic, fatal, nonsuppurative meningoencephalitis in alpacas and sheep.