Latent Epstein-Barr virus (EBV) infection is associated with a variety of malignancies and other diseases. Highly restricted viral antigen expression and low viral genome copy number in infected tissues impede conventional immunohistochemical or in situ hybridization approaches to the detection of virus in these tissues. In situ hybridization detection of two small but very abundant nuclear RNAs known as the EBERs serves as an alternative approach. The EBERs are stable over time and can be detected in all common fixatives. This technique facilitates characterization of the cellular locus of latent EBV infection in histologically complex tissues, such as Hodgkin's disease and angioimmunoblastic lymphadenopathy with dysproteinemia.