Quantitative PCR (QPCR, or real time PCR (rtPCR)) has emerged as a powerful virologic technique for measuring viral replication and viral loads in humans and animal models. We have developed a QPCR assay to accurately quantify lymphocytic choriomeningitis virus (LCMV) in infected mice. We first validated this assay using plasmid DNA and LCMV viral stocks. We then demonstrated that the LCMV QPCR assay can detect LCMV in serum and tissues of chronically infected mice (LCMV-clone 13), with greater sensitivity than conventional plaque assay. Subsequently, we demonstrated that the QPCR assay can detect LCMV in tissues of CD40L(-/-) mice during a low grade chronic infection with LCMV Armstrong. Finally, we improved the assay further such that it was approximate 1000-fold more sensitive than plaque assay for detection of the presence of LCMV in tissue.