Obesity is one of the dramatic health issues affecting this country and exercise is a well-established intervention strategy. While exercise-by-genotype interactions have been shown in humans, overall little is known. Using the natural negative geotaxis of Drosophila melanogaster, an important model organism for the study of genetic interactions, a novel exercise machine, the TreadWheel, can be used to shed light on this interaction. The mechanism for inducing exercise is inherently low impact thus minimizing confounding effects of other stressors. Using this machine, we are able to assess large cohorts of adult flies from eight genetic lines for their response to exercise over one week of training. We have measured their triglyceride, glycerol, protein, glycogen content, and body weight, as well as their climbing ability and feeding behavior in response to exercise, and generally find that exercised flies are more fit than unexercised flies. We have also assessed expression in a panel of genes known to be associated with respiratory fitness and find that many of these genes show expected changes in expression level with exercise. In addition to demonstrating and overall effect of exercise on flies, we find significant genotype-by-exercise interaction effects for many of the measured phenotypes, and those differences can be partially linked to innate differences in flies' persistence in maintaining activity during exercise bouts. With this study, we have established the TreadWheel as useful tool to study exercise effects in flies, shown significant genotype-specific impacts of exercise, and have laid the ground work for more extensive studies of how genetics, environment, and aging interact with exercise to influence metabolic fitness in Drosophila.