BACKGROUND: Genital infection by herpes simplex virus (HSV)-2 offers a unique model for study of the effects of a remitting and exacerbating infection on the survival and persistence of antigen-specific T cells. METHODS: We used complementarity-determining region 3 (CDR3) length analysis to examine the complete T cell receptor (TCR) beta -chain repertoire in skin-lesion biopsy samples from subjects with genital herpes. RESULTS: We found that herpetic skin lesions consistently demonstrated oligoclonal CDR3 DNA length distribution, indicating the presence of T cell expansions. Sequence analysis of representative HSV-specific lesional CD4(+) cell clones and TCR beta -variable (TCRBV) sequencing confirmed that the oligoclonal expansions were largely related to HSV-specific T cell proliferation. To assess the persistence of HSV-specific CD4(+) cells that localize to genital lesions, we developed a sensitive and highly specific clonal tracking technique using a combination of TCRBV-specific polymerase chain reaction, followed by liquid hybridization with clonotype-specific probes. CONCLUSION: Two different patterns of clonal persistence were observed. Some long-lasting clones appear to home to different epithelia, such as skin and genital mucosa, and to circulate in the peripheral blood, whereas others detected in lesions were absent or very rare in the peripheral blood.