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Multidrug resistance is among the most pressing obstacles in cancer treatment today. Resistance is thought to arise from the ability of cancer stem cells to efflux therapeutic molecules using a collection of membrane proteins called ATP-binding cassette (ABC) transporters. There is strong interest in targeting ABC transporters to preserve and improve drug efficacy and reduce cancer recurrence. Many studies have been performed in vitro using cultured cell lines, but currently there is a lack of simple models in which to study ABC transporters in vivo. As a solution, I propose to use the fruit fly Drosophila melanogaster for the study of ABC transporters, and specifically the D. melanogaster testis stem cell niche—one of the best-characterized adult stem cell niches. Stem cells have several traits in common with cancer cells, including the ability to divide indefinitely, the ability to give rise to many different kinds of daughter cells, and chemoresistance. In invertebrates there is mounting evidence for a role ABC transporters play in insecticide resistance, but to date there is no peer-reviewed evidence for invertebrate stem cell drug resistance in the literature. Here, I present evidence of cytotoxic drug efflux in the germline stem cells of the D. melanogaster testis. This was accomplished by feeding the chemotherapy drug doxorubicin to wild type flies for two days and measuring fluorescence levels using confocal microscopy. Using enhancer trap lines, I also present ABC transporter expression evidence in both the germline and cyst lineages of the testis. Finally, through RNAi knockdown of several ABC transporters, I present evidence of their contribution to germline stem cell drug efflux. I also report unexpected phenotypes in the male germline resulting from the knockdown of two ABC transporters, CG32901 and CG3164, which points to a role for these proteins in development of the normal testes niche.