The oxazaphosphorines including cyclophosphamide and ifosfamide represent an important group of drugs because of their wide use as antitumor and immuno-modulating agents. This review highlights the effects of polymorphisms of genes involved in the action, distribution, metabolism, and transport of oxazaphosphorines on their pharmacokinetic variability and therapeutic outcomes. Emerging data indicate that polymorphisms of genes encoding cytochrome P450 (CYP) enzymes (CYP3A4, CYP2B6, and CYP2C9), aldehyde dehydrogenases (ALDH1A1, ALDH3A1), glutathione Stransferases (GSTT1, GSTM1, GSTP1), multidrug resistance-associated proteins (ABCC1 and ABCC2), and methylguanine- DNA methyltransferase (MGMT) play an important role in the wide interindividual pharmacokinetic variability and altered clinical outcome of oxazaphosphorine chemotherapy. For example, CYP2B6*5 (C1459T giving rise to an Arg487Cys substitution) and CYP2C19*2 (C430T) are associated with altered response, toxicity, and survival in patients with proliferative lupus nephritis when treated with pulse cyclophosphamide regimens. In paediatric patients with corticosteroid- sensitive nephrotic syndrome, treatment with cyclophosphamide in patients with a GSTM1 null polymorphism gave a significantly higher rate of sustained remission than in patients with the heterozygous or homozygous GSTM1 wildtype. Preliminary preclinical and clinical studies indicate that a number of genetic polimorphisms can affect the disposition and action of oxazaphosphorines, causing large interpatient variability in their pharmacokinetics, response rate and toxicity. A full identification of the role of these genetic polymorphisms would allow the identification of useful and novel strategies to overcome the resistance and toxicity of oxazaphosphorines and to design optimal therapeutic regimens.