We reported two cases with germ cell tumor in which new preliminary treatment trials were performed by chemotherapy using anti-cancer drug selected on the basis of multidrug resistance gene mRNA expression, such as MDR1, MRP1, MRP2, MXR1, MGMT, GST pi and TopoII alpha, from RT-PCR assay. A 28-year-old male had gradually developed DI. MR imaging revealed enhanced tumors in the medulla oblongata, the pineal region and the suprasella region. Biopsy of tumor in the medulla oblongata demonstrated germinoma histologically. RT-PCR assay of this tissue revealed overexpression of MRP1, MGMT and GST pi mRNA, but neither MDR1, MRP2 nor MXR1 was observed. The patient was successfully given carboplatin, mitoxanthrone and ifosphamide after irradiation. A 15-year-old male was admitted to our hospital with high intracranial pressure syndrome. MR imaging revealed enhanced tumor in the pineal region. The tumor was diagnosed as a malignant germ cell tumor, histopathologically. RT-PCR assay of this tissue revealed overexpression of MRP1, MRP2, MXR1, MGMT and GST pi mRNA. Only MDR1 was not expressed. The patient was treated by irradiation including radiosurgery combined with chemotherapy, given cisplatin, etoposide and ifosphamide (ICE regimen), but he died because of progressive disease such as CSF dissemination. It seems that preliminary individual adjuvant chemotherapy based on mRNA expression of drug-resistance gene is available for the treatment of germ cell tumors.