Vibration measurement techniques can be categorized into contact-type and non-contact-type techniques. These types of techniques can add mass-loading to a lightweight structure resulting in the negative performance of a structure, because sensors, high contrast speckles or targets should be mounted on a structure. Moreover, non-contact-type vibration measurement techniques have only been tested to detect vibrations using a single camera. As the vibrations occurring at the opposite sides of a rotating structure in a region of interest (ROI) can be different from each other. For 3-dimensional (3D) vibration measurement, the same position in videos acquired from two cameras should be used. Because the videos acquired by two cameras placed perpendicular to the structure can be used to detect the vibrations in the x-direction as well as y-direction. In this study, an epipolar line-based corresponding point selection on a rotating cylindrical structure was performed, to extract the same ROIs from videos recorded by two cameras. A fundamental matrix was constructed by using the targets attached on the structure and in the background. The coordinates of the mid-pixel of the ROI in a video acquired by one camera was used to determine the epipolar line for the same ROI in the video acquired by another camera. Then an edge-based vibration measurement technique was applied to measure the vibration in the extracted ROIs. The results were used to reconstruct a 3D vibration signal. The 3D vibration measurement results can be used to effectively recognize the deformations resulting in the negative performance of a structure.