The contamination of apheresis products with tumor cells was evaluated in patients undergoing autologous peripheral blood stem cell transplantation for germ cell tumors. A blinded, retrospective analysis was performed on 63 apheresis products from 28 patients using the PCR and primers for beta human chorionic gonadotropin (beta-HCG). Of the 20 patients with beta-HCG-secreting tumors, 8 apheresis products from 7 patients were PCR positive. PCR was negative in the 8 patients whose tumors did not secrete beta-HCG. Twenty-two apheresis products from patients with lymphoma and breast cancer were negative for beta-HCG expression. Evaluating the 20 patients with beta-HCG-secreting tumors, 100% of PCR-positive patients had elevated serum beta-HCG at the time of apheresis compared to 46.2% of PCR-negative patients (P = 0.04). A positive PCR was also associated with a higher serum beta-HCG at diagnosis (P = 0.03). Patients receiving a PCR-positive product had a higher relapse rate (85.7 versus 61.5%) and were more likely to have visceral metastasis (100 versus 61.5%), although the numbers did not reach statistical significance (P = 0.35 and 0.11, respectively). The finding of beta-HCG mRNA in apheresis products strongly suggests the presence of circulating tumor cells in a significant number of germ cell patients undergoing autologous transplantation. This assay may be useful in monitoring attempts at tumor cell depletion and in developing improved prognostic models for assessing risk of relapse after transplantation.