Resistance to cyclophosphamide therapy continues to be a major reason for treatment failure. This chapter covers some of the mechanisms implicated in resistance to the toxic and mutagenic effects of cyclophosphamide therapy in the laboratory and clinic. Since resistance is likely to be the result of a number of interrelating factors, this chapter evaluates the contribution of both glutathione and DNA repair processes to cyclophosphamide resistance. Glutathione appears to be involved directly in the detoxification of cyclophosphamide and metabolites and may play a more indirect role in other processes. The ability of the cell to repair cyclophosphamide-induced DNA lesions, possibly through nucleotide excision repair or other processes, may be a key contributor to drug resistance. Interestingly, the presence of the repair enzyme, O6-alkylguanine-DNA alkyltransferase, long thought to be involved with resistance to methylating and chloroethylating agents, may also contribute to resistance to the cytotoxic and mutagenic effects of cyclophosphamide.