Alphaviruses (Togaviridae) infect wild birds, but clinical illness and death attributable to virus in naturally infected birds is rarely reported, particularly for small passerine species or nestlings. Buggy Creek virus is a unique alphavirus in the Western equine encephalomyelitis virus (WEEV) complex that is vectored by the cimicid swallow bug (Oeciacus vicarius), an ectoparasite of the colonially nesting Cliff Swallow (Petrochelidon pyrrhonota) and the introduced House Sparrow (Passer domesticus). While sampling birds for Buggy Creek virus (BCRV) during the summers of 2007 and 2008, we discovered large numbers of clinically ill or dead House Sparrow nestlings. Ill nestlings exhibited ataxia, torticollis, paresis, and lethargy. Histologic examination revealed that encephalitis was the most common finding, followed by myositis, myocarditis, and hepatic changes, but pathology was highly variable. We isolated BCRV from brain tissue in most of the ill or dead nestlings, and from blood, liver, kidney, spleen, lung, feather pulp, and skin in some birds. To our knowledge, this is the first report of clinical illness, gross pathology, and histopathology for a WEEV-complex alphavirus in a field-collected passerine species.