Disseminated tumor cells (DTC) in peripheral blood are considered as the cause for the formation of metastases. Furthermore, their presence is increasingly regarded as a prognostic factor. However, genomic alterations that characterize DTC are still unknown. In order to assess the status of microsatellite instability (MSI) and loss of heterozygosity (LOH), a certain amount of DNA is required, but that is not available from only a limited number of DTC isolated from peripheral blood. In our study, we have applied the improved primer extension preamplification (IPEP) in order to amplify the genomic DNA from DTC of renal cell carcinoma patients, breast carcinoma patients and prostate carcinoma patients preceding the investigation of MSI and LOH in these cells. The DNA was subsequently used to determine the status of several microsatellite markers, e.g. MycL1, Rb, and p53 Alu. The results were compared to those of the primary tumor tissue, adjacent normal renal tissue, as well as, from peripheral blood lymphocytes. Furthermore we have determined molecular alterations on DNA-level (LOH/MSI, methylation status, SNP309) and protein level (expression of survivin, uPA, uPAR und PAI) in disseminated tumor cells and tumor tissue. The results were correlated to essential clinical parameters as tumor size, grading, stage, lymph nodes, metastases and overall surviving.