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Second primary malignancy (SPM) is a well-known cause of death in head and neck cancers. Recently, with reports of many incidences of human papilloma virus (HPV) associated SPM,the disease has been widely investigated. We report a HPV-positive tracheal cancer in a 49-yearoldmale who had been diagnosed with HPV-positive squamous cell carcinoma of the righttonsil within intervals of two years. In this case, the metachronous tracheal cancer lesion aswell as the primary tonsillar cancer showed the same subtype HPV-16.