Herpes simplex virus (HSV) establishes latent infection in the sensory neuron and possibly in non-neuronal tissue, particularly the cornea. During latency only one region of the HSV genome is transcribed, producing RNAs known as latency associated transcripts (LAT). The gene for LAT overlaps with the HSV gene for the protein ICPO in the downstream regions of both genes. Latency can occur in the absence of LAT. This study reports the detection of ICPO/LAT and thymidine kinase (TK) gene fragments by the polymerase chain reaction in DNA extracted from the corneas and trigeminal ganglia of latently infected rabbits. Both genes were detected in four of four trigeminal ganglia tested and in three of five corneas tested. More importantly, this study reports the first detection of LAT in RNA extracted from 9% of corneas from latently infected rabbits (n = 22) by the polymerase chain reaction. LAT was detected in RNA from 100% of the corresponding trigeminal ganglia (n = 22). Although LAT is not essential for latency, it remains the only known molecular marker for latent HSV infections. Detection of LAT in these rabbit corneas suggests that HSV latency may occur in this non-neuronal tissue and that reactivation from non-neuronal tissue may occur at a low frequency in animals in which HSV latency has been established.