Mitochondria are subcellular organelles that synthesize ATP, generate reactive oxygen species (ROS), and control cellular fates such as apoptosis and aging. Mitochondria generate different amounts of ROS in association with their morphologies. Cyclic stretch is a mechanical stimulation exerted on cells due to arterial pulsation, and induces cells to generate mitochondrial ROS. Therefore, one can speculate that morphological changes of mitochondria may play a role in mitochondrial ROS generation in cells under cyclic stretch. However, whether the morphologies of mitochondria are actually altered under cyclic stretch remains unclear. This study attempted to answer this question by time-lapse imaging the morphological dynamics of mitochondria in bovine aortic endothelial cells (BAECs) subjected to two levels of uniaxial cyclic stretch: (1) a physiologic level (5% at 1 Hz) for 1 hour, and (2) a supra-physiologic level (20% at 1 Hz) for 1 hour. Mitochondria were stained with Mito-tracker Orange, and MicroP software and FibrilTool were used for mitochondrial alignment and length analyses. No clear changes in the average length of mitochondria were observed at the physiological level of stretch (5%) compared to no stretch (0%), while the average length was decreased by the supra-physiological level of stretch (20%). In addition, cellular alignment was not different between 0% and 5% stretches, but the cells became perpendicularly aligned in the direction of stretch when 20% stretch was applied. Cellular circularity was not significantly different among the three levels of cyclic stretch. Thus, BAECs exhibited changes in both mitochondrial dynamics and cellular remodeling dynamics under 20% stretch, but showed no changes in both under 5% stretch. The results indicate that changes in morphological dynamics of mitochondria correlate with changes in cellular dynamics, particularly change in cellular alignment.