The presence of wild-type herpes simplex virus type 1 (HSV-1) and several latency associated transcript (LAT) region mutants within the trigeminal ganglia (TG) of latently infected mice was examined. A combination of methods including conventional in situ hybridization to detect viral LAT and an in situ DNA polymerase chain reaction (PCR) to detect viral DNA was used. These data show that, for all virus strains in which a comparison was possible, the population of neurons expressing detectable levels of LAT was approximately one-third the total number of viral DNA-containing cells. In addition, in situ PCR analysis revealed that mutants such as 17 delta Sty. 17 delta BstE, and 17 delta S/N, which contain deletions within the LAT locus which do not affect the kinetics of viral reactivation from explanted murine TG, are present in as many neurons as wild-type virus. This was true regardless of the ability to induce accumulation of intact 2.0-kb LAT. On the other hand, mutant 17 delta N/H, which contains a deletion removing the LAT promoter and surrounding genomic region and reactivates slowly from explanted TG, was present in only one-sixth as many neurons as wild-type virus. These data show that detection of mutants unable to synthesize or accumulate 2.0-kb LAT (such as 17 delta N/H) is possible with in situ DNA PCR and that the slow reactivation phenotype of 17 delta N/H correlates with a reduced number of HSV DNA-containing neurons.