There is no effective treatment for late stage and metastatic cancers of colorectal, prostate, pancreatic, breast, glioblastoma and melanoma cancers. Novel treatment modalities are needed for these late stage patients because cytotoxic chemotherapy offers only palliation, usually accompanied with systemic toxicities and poor quality of life. Gene directed enzyme prodrug therapy (GDEPT), which concentrates the cytotoxic effect in the tumor site may be one alternative. This review provides an explanation of the GDEPT principle, focusing on the development, application and potential of various GDEPTs. Current gene therapy limitations are in efficient expression of the therapeutic gene and in tumor-specific targeting. Therefore, the current status of research related to the enhancement of in situ GDEPT delivery and tumor-specific targeting of vectors is assessed. Finally, GDEPT versions of stem cell based gene therapy as another potential treatment modality for progressed tumors and metastases are discussed. Combinations of traditional, targeted, and stem cell directed gene therapy could significantly advance the treatment of cancer.