Recent estimates show that more than 78.6 million adults are obese in the United States with the annual medical cost at $147 billion dollars in 2008. The most common treatments for obesity come in the form of a dietary change or an increase in physical activity (exercise). Despite the popularity of exercise as a treatment for obesity, very little is known about how an individual’s genetic background impacts his/her response to exercise. This has become increasingly relevant as new studies have indicated that up to 20% of the population may be “exercise non-responders”, individuals who are programmed – genetically or epigenetically – to have weak or absent metabolic responses to exercise. In order to elucidate the genetic mechanisms underlying exercise response, we have developed an innovative exercise system for Drosophila melanogaster named the Rotating Exercise Quantification System (R.E.Q.S.). This system allows for the real-time quantification of exercise in Drosophila. One interval and one continuous exercise regime were performed on three fly lines from the Drosophila Genetics Reference Panel 2 (DGRP2). Our results show that there is significant variability in exercise levels between these lines, enough so to perform Genome Wide Association Studies (GWAS) using the entire panel of 200 lines to identify candidate genes. This study validates the use of rotation-based exercise and demonstrates the potential for Drosophila as a model in the field of exercise genetics.