An immunohistochemical (IHC) assay was developed for the detection of eastern equine encephalomyelitis (EEE) virus antigen in formalin-fixed, paraffin-embedded tissues. All cases of EEE diagnosed at the Michigan State University Animal Health Diagnostic Laboratory from 1991 through 1994 were evaluated. The diagnosis was based on histopathologic examination of the brain and confirmatory virus, isolation. Sections of cerebrum from 26 equids and 5 birds were assessed by IHC. Histologically normal brain tissues from 2 horses and 1 pheasant and brain tissues from 2 cases of equine neurologic disease with diagnoses other than EEE served as negative controls. The IHC assay was based on standard streptavidin-biotin technology, using a commercially available kit and a monospecific polyclonal primary antibody preparation derived from murine ascitic fluid. Nineteen of 20 equids and all 5 birds positive by histopathology and virus isolation were positive for EEE virus antigen by IHC. Three equids with histologic lesions compatible with a diagnosis of EEE but negative by virus isolation also were negative for virus antigen by IHC. In 3 other equids, histopathology and IHC were positive for EEE, but virus isolation was not attempted because of contamination of the brain specimen. The IHC assay of formalin-fixed, paraffin-embedded brain tissues for EEE virus antigen is a rapid, effective test for confirming a histopathologic diagnosis of EEE, and assay results correlate well with virus isolation results.