The oxazaphosphorines cyclophosphamide (CP) and ifosfamide (IF) are alkylating agents that require bioactivation via cytochrome (CYP) P450 isoenzymes including CYP2C9 enzymes. The present study investigated CYP2C9 in regard to its allelic variants in 23 tumor samples (10 breast tumors, 1 breast tumor cell line, 5 brain tumors, 7 glioma cell lines) with restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR). The mutant alleles of CYP2C9 were residue 144 (Arg (*1)/Cys (*2)), residue 358 (Tyr/Cys), residue 359 (Ile/Leu (*3)) and residue 417 (Gly/Asp). The frequencies of the CYP2C9*1, CYP2C9*2 and CYP2C9*3 alleles in the cancer samples examined were found to be 0.848, 0.152 and 0.043, respectively. No sample revealed a mutation at residue 358 or 417. Comparing breast with brain tumors, brain tumors seemed to reveal a higher incidence of heterozygotes (5/12 compared to 2/11) at residue 144 and, with regard to residue 359, a lower incidence of heterozygotes (0/12 compared to 2/11). In summary, our data indicate that in tumor material, as in healthy material, the same allelic variants of CYP2C9 occur. Compared to healthy tissue, tumor material seemed to reveal a higher incidence of the *2 allele, but a significant difference could not be established. Our results show that brain and breast tumor samples appeared to differ in their frequency of heterozygotes at residues 144 and 359. This might also have an impact on intratumoral oxazaphosphorine metabolism.