For patients with head and neck squamous cell carcinoma (HNSqCC), the development of squamous cell carcinoma (SqCC) in the lung may signal a new primary or the onset of metastatic dissemination. Although the distinction influences prognosis and therapy, it may not be straightforward on histologic or clinical grounds. The human papillomavirus (HPV) is an etiologic agent for SqCCs arising from the oropharynx but not for SqCCs arising from other head and neck sites. For patients with HNSqCC who develop a lung SqCC, HPV analysis could be useful in establishing tumor relationships. High-risk HPV in situ hybridization was performed on 54 lung SqCCs from patients with a previously diagnosed HNSqCC and on 166 primary lung carcinomas from patients without a prior HNSqCC. HPV was detected in 11 of 220 (5%) cases. All HPV-positive cases were from patients with a prior oropharyngeal SqCC. For the paired oropharyngeal and lung SqCCs, HPV status was concordant in 95% of cases. Time from treatment of HPV-positive oropharyngeal carcinomas to detection of lung carcinoma ranged from 1 to 97 months (mean, 36 mo). Two HPV-positive cancers were detected in the lung 8 years after treatment of the oropharyngeal primary. Despite the long interval, E6 sequencing analysis of 1 of these paired samples confirmed that the tumors harbored the same HPV-16 variant. HPV does not seem to play a role in the development of primary lung cancer. For patients with oropharyngeal SqCC who develop lung SqCC, HPV analysis may be helpful in clarifying tumor relationships. These relationships may not be obvious on clinical grounds, as HPV-related HNSqCC may metastasize long after treatment of the primary tumor.