This thesis presents online 3D reconstruction and ground segmentation using unmanned aerial vehicle (UAV) based stereo vision. For this purpose, a long baseline stereo vision system has been designed and built. Application of this system is to work as part of an air and ground based multi-robot autonomous terrain surveying project at Unmanned Systems Lab (USL), Virginia Tech, to act as a first responder robotic system in disaster situations. Areas covered by this thesis are design of long baseline stereo vision system, study of stereo vision raw output, techniques to filter out outliers from raw stereo vision output, a 3D reconstruction method and a study to improve running time by controlling the density of point clouds. Presented work makes use of filtering methods and implementations in Point Cloud Library (PCL) and feature matching on graphics processing unit (GPU) using OpenCV with CUDA. Besides 3D reconstruction, the challenge in the project was speed and several steps and ideas are presented to achieve it. Presented 3D reconstruction algorithm uses feature matching in 2D images, converts keypoints to 3D using disparity images, estimates rigid body transformation between matched 3D keypoints and fits point clouds. To correct and control orientation and localization errors, it fits re-projected UAV positions on GPS recorded UAV positions using iterative closest point (ICP) algorithm as the correction step. A new but computationally intensive process of use of superpixel clustering and plane fitting to increase resolution of disparity images to sub-pixel resolution is also presented. Results section provides accuracy of 3D reconstruction results. The presented process is able to generate application acceptable semi-dense 3D reconstruction and ground segmentation at 8-12 frames per second (fps). In 3D reconstruction of an area of size 25 x 40 m2, with UAV flight altitude of 23 m, average obstacle localization error and average obstacle size/dimension error is found to be of 17 cm and 3 cm, respectively.