Drosophila melanogaster presents itself as a powerful model for studying the somatic stem cells of the gut and how bacteria affect intestinal homeostasis. The Gal4/UAS/Gal80 (ts) system allows for temporally controlled expression of fluorescent proteins, RNAi knock-down, and other genetic constructs targeted to specific cell populations in the midgut. Similarly, FLP/FRT-mediated somatic recombinations in intestinal stem cells (ISCs) are utilized to visualize and analyze the clonal lineages of individual or populations of stem cells. Live imaging microscopy and immunofluorescence allow both qualitative and quantitative characterization of stem cell shape, proliferation, and differentiation. Here, we detail the use of these tools and techniques for studying gut performance during and following a bacterial infection in the adult fruit fly.