Nucleic acid hybridization techniques have contributed significantly to the understanding of gene organization, regulation and expression. In the context of persistent or latent viral infections, hybridization with specific labelled probes represents the most sensitive assay presently available for detection of viral genomes. During the course of persistence, viral genomes may exist in multiple and yet quite segregated areas in an infected host, but examination of all tissues remains difficult and time-consuming. At present, the application of hybridization assays to in vivo infections requires either chemical extraction of nucleic acid coupled with dot-blot and gel transfer techniques or in situ hybridization to cryostat tissue sections. In both cases, selected tissues must be removed by dissection before analysis. We describe here a procedure which allows efficient and reproducible screening of all tissue in an infected host. Our technique allows detection of viral genetic material in whole-body sections of infected mice, and provides the first evidence in vivo for accumulation of viral genetic material with a parallel decrease in infectious virus during persistent virus infection. This technique should be widely applicable to studies of developmental regulation of gene expression, for monitoring locations of gene expression in transgenic mice and for analysis of molecular mechanisms in pathogenesis.