A polymerase chain reaction (PCR) assay was developed to detect the thymidine kinase gene of feline herpesvirus 1 (FHV-1) and to study the active and latent carrier state in a group of naturally FHV-1 infected specific pathogen free (SPF) cats. The detection limit of PCR products on ethidium bromide stained gels was 390 fg or about 3 x 10(3) copies of the FHV-1 genome. The PCR was 25% more sensitive than conventional cell culture based virus isolation techniques in detecting FHV-1 in oral/ocular swabs and 100 times more sensitive in detecting virus in cell culture supernatants. Sites of FHV-1 latency in FHV-1 carriers as determined by PCR were mainly tissues of the head, especially the trigeminal ganglia, optic nerves, olfactory bulbs and corneas. Oral fauces, salivary glands, lacrimal glands, cerebellum and conjunctiva were less consistently positive. The cerebral cortex, thymus, trachea, lung, liver, spleen, kidney, and peripheral blood mononuclear cells were consistently negative for FHV-1 genome. The distribution of FHV-1 DNA in the tissues of the head was similar whether or not corticosteroid-induced virus shedding was occurring at the time the tissues were collected. Infectious virus was never recovered from tissue homogenates regardless of the PCR status of the tissues.