Human cytomegalovirus (HCMV) and human immunodeficiency virus (HIV) cause severe disease. The identification of these viruses in clinical specimens and understanding the progression of infection and diseases relating to HCMV and HIV are essential to develop effective means for treatment and prevention. Here we describe the application of molecular probes to the diagnosis and pathogenesis of HCMV and HIV. In situ hybridization and the amplification procedure of polymerase chain reaction are used to detect both viruses; these techniques have provided important information regarding the pathogenesis of HCMV and HIV. A new technique, target cycling, may also prove useful for the detection of viruses by enriching for target sequences. The continued application of molecular probes to pathogenetic studies of HCMV and HIV promises to further our knowledge of these viruses, and of their interaction.