Human papillomavirus (HPV) DNA has been shown by molecular hybridization studies to persist in both recurrent and metastatic disease in tumors of the female genital tract. We report here the use of the polymerase chain reaction to identify HPV DNA in material from fine-needle aspirates (FNA) of recurrent or metastatic lesions to document the primary malignancy arising in the lower genital tract. Fine-needle aspirates of suspected recurrent or metastatic tumors were obtained from nine patients with carcinoma of the lower genital tract and five patients with malignancies that have not been associated with HPV. DNA was extracted from the FNA and tissue block, when available, and amplified with HPV 6, HPV 16, and HPV 18 specific primers. In eight of the nine tumors from the lower genital tract, HPV DNA was identified in both the primary and metastatic lesions. In every case the HPV genotype was identical. One cervical carcinoma and five non-HPV associated tumors were negative for papillomavirus DNA. This study demonstrates that molecular hybridization techniques can be useful in identifying the source of a metastasis and have the potential to diagnose the presence of metastatic disease by detecting HPV DNA even when the cytologic criteria are equivocal.