We examined the possibility of using microsatellite and mitochondrial DNA polymorphisms as markers to detect the clonal origin of tumor cells found in the same patient. We considered two children with complex tumor diseases: one with supratentorial primitive neuroectodermal tumors (PNET) and a hepatic rhabdoid tumor and another with brain and abdominal rhabdoid tumors. In the first patient we found an mtDNA cytosine insertion both in the normal tissue and in the primary tumor, whereas in the hepatic tumor we detected an insertion of 2 cytosine. In the second child, who had a constitutional mutation of hSNF5/INI-1, we identified the same mtDNA pattern both in normal tissue and in the abdominal tumor but not in the brain tumor, which presented three different mtDNA polymorphisms. Thus, we demonstrated the same clonal origin for tumors in the first patient and different clonal origins of the tumors in the second patient. At times it is very difficult to discriminate two neoplastic lesions or metastatic diseases by using only histopathologic techniques. Molecular examination of clonality is a useful tool to obtain information about the origin of synchronous and/or metachronous tumors found in the same patient.