A 55-year-old woman was admitted for an evaluation of a mediastinal mass, bilateral cervical lymphadenopathy and a left breast tumor. Although pathology revealed a diagnosis of breast cancer, the cervical lymph nodes differed from the breast lesion. An anaplastic lymphoma kinase (ALK) gene analysis revealed ALK rearrangement in the cervical lymph nodes only, which were therefore diagnosed as reflective of metastasis of lung adenocarcinoma. The mediastinal tumor was also diagnosed as an ALK-positive lung adenocarcinoma based on its therapeutic response. ALK gene analyses can be used to identify primary lesions in patients with cancers of unknown primary sites.