Necrosis and apoptosis during acute myocardial infarction result in part from the inability of hy- poxic cardiac myocytes to match ATP supply and demand. In contrast, hypoxia-tolerant organisms, such as Drosophila, can rapidly regulate cellular metabolism to survive large oxygen fluctuations. A genetic screen of fly heart function during acute hypoxia can be an unbiased way to discover essential enzymes and novel signaling proteins involved in this response. We have developed a pro- totype to show proof of concept for a genome-scale screen, using computer automation to rapidly gather in vivo hypoxic heart data in adult Drosophila. Our system automatically anesthetizes flies, deposits them on a microscope slide, and locates the heart organ of each fly. The system then applies a hypoxia stimulus, acquires time-space (M-mode) images of the heart walls, and analyzes heart rate and rhythm. The prototype can produce highly controlled measurements of up to 55 flies per hour, which we demonstrated by characterizing the effect of temperature, oxygen con- tent, and genetic background on the hypoxia response. We discuss the possible applications of a genome-wide cardiac phenotype data set in systems biology analyses of hypoxic metabolism, using genome-scale interaction networks and constraint-based metabolic models.