Physiological status, particularly dietary input, has major impacts on the Drosophila melanogaster ovarian germline stem cell lineage. In addition, inter-organ communication plays an essential role in coordinating whole-organism responses to changes in physiology. For example, nutrient-sensing signaling pathways function within the fat body to regulate germline stem cells and their progeny in the ovary. Together with its incredible genetic and cell biological toolkits, Drosophila serves as an amenable model organism to use for uncovering molecular mechanisms that underlie physiological control of adult stem cells. In their new methods chapter titled "Methods to Analyze Nutritional and Inter-Organ Control of Drosophila Ovarian Germline Stem Cells", graduate students Chad Simmons, Tancia Bradshaw, and their mentor Dr. Alissa Armstrong describe a general dietary manipulation paradigm, genetic manipulation of adult adipocytes, and whole-mount ovary immunofluorescence to investigate physiological control of germline stem cells.