Most current studies of ROS production report globally averaged measurements within the cell; however, ROS can be produced in distinct subcellular locations and have local effects in their immediate vicinity. A microfluidic platform for high-throughput single cell imaging allows mitochondrial ROS production to be monitored as varying in both space and time. Using this systems biology approach, single cell variability can be viewed within a population. We discuss single cell monitoring of contributors to mitochondrial redox state - mitochondrial hydrogen peroxide or superoxide - through the use of a small molecule probe or targeted fluorescent reporter protein. Jurkat T lymphoma cells were stimulated with antimycin A and imaged in an arrayed microfluidic device over time. Differences in single cell responses were observed as a function of both inhibitor concentration and type of ROS measurement used.