It is not uncommon for patients with urothelial cancer to have synchronous and metachronous multifocal invasive tumors of the bladder and upper urinary tract. If a metastatic lesion becomes evident in such a patient, the origin of the metastasis is often not determinable using conventional histopathologic examination of the surgical or autopsy specimen. Here, we report a patient in whom the clonal relationship among the histologically undistinguishable multifocal urothelial cancers and metastatic tumors could be clarified by molecular genetic analysis. Furthermore, the potential role for each genetic alteration in the multifocal and metastatic tumor development and the treatment efficacy for each multifocal tumor were also clearly demonstrated.