This study aims to highlight the differences, in terms of robustness and efficiency, of the use of LIDAR point clouds compared to dense image matching (DIM) point clouds at urban areas that contain buildings with complex structure. The application is conducted over an area in the Greek island of Milos using two different types of data: (a) a dense point cloud which extracted by DIM using a variation of the stereo-method semi-global matching (SGM) at RGB digital aerial images, and (b) a georeferenced LIDAR point cloud. For the case of the DIM point cloud, the following steps were applied: aerial triangulation, rectification of the original images to epipolar images, extraction of disparity maps and application of a 3D similarity transformation. The evaluations that were executed included urban and rural areas. At first step, a direct cloud-to-cloud comparison between the georeferenced DIM and LIDAR point clouds was carried out. Then, the corresponding orthoimages generated by the DIM and LIDAR point clouds undergo a quality control. Although the results show that the LIDAR point clouds respond better at such complex scenes compared to DIM point clouds, the latter gave promising results. In this context, the Quality Assurance issue is also discussed so as to be more efficient towards the challenge of the increasingly greater demands for accurate and cost effective applications.