The sophisticated genetic tools available in Drosophila, coupled with the evolutionary conservation of biological processes found in higher organisms, including humans, should encourage the use of whole organism in drug discovery, diet, and toxicology. For high-throughput work, this requires plate formats compatible with standard equipment, minimization of handling, and low volume feeding. To meet these design specifications, we have developed a 3D printed 96-well system called the Whole Animal Feeding Flat (WAFFL). The WAFFL is an apparatus that enables the housing and feeding of flies while reducing the number of manipulations. It has four main units for: 1) food 2) feeder (housing) 3) receiver and 4) transfer adapter. The liquid food (<10ul) is provided to the fly in a round bottom 96 well plate. The feeder plate is an array of 96 deep square shaped chambers where a single fly is housed that tightly fits into the food plate. The feeder plate includes inner ledges upon which a housed fly can perch while extending its proboscis through narrow capillary ports with liquid food. Cameras integrated into the system allow monitoring of behavior. The transfer adapter allows the interconnection of the chambers of the feeder plate to a receiver plate to harvest the flies by centrifugation to a standard deep well plate for homogenization and assay preparation. The WAFFL facilitates the transfer of flies from one condition to another in seconds by simply placing the feeder plate on a different microplate with the condition of interest without disturbing the flies. To ensure that compound doses are delivered at the same time, we used 6 hr treatments on starvation media, followed by 1 hr of feeding. A bolus of food (with dye) was observed and transit time through the gut is < 3 hrs. We have performed several small screens (600 - 800 flies) for exposure to dimethyl sulfoxide (DMSO), ethanol, and different diets. We will present time-course results (~600 flies) on the effect of DMSO on gene expression profiles following exposure to different concentrations of DMSO .The scalable WAFFL system allows for automated handling of individual flies exposed to different foods, drugs, and compounds, providing a unique high-throughput platform for drug screening in flies. The WAFFL and flies are a limitless discovery duo.