In the field of archaeological surveying, remote sensors and especially photogrammetric and laser scanner systems are widely used to create 3D models. The use of photogrammetric surveying with UAVs (Unmanned Aerial Vehicles), combined with Computer Vision algorithms, allows the building of three-dimensional models, characterized by photo-realistic textures. The choice of which method to use mainly depends on the complexity of the investigated site, the accuracy requirements and the available budget and time. The different components of the UAV system determine its characteristics in terms of performance and accuracy, therefore define its quality and the cost too. This study presents an assessment of the accuracy of point clouds derived by two UAV systems, a commercial quadcopter (DJI Phantom 3 Professional), a professional assembled hexacopter, and by a TLS (Terrestrial Laser Scanner) in order to compare photogrammetric and laser scanner data for archaeological applications. In this paper, we present a case study to compare and analyse the metric accuracy of the point clouds and the distribution of the GCPs (Ground Control Points). This accuracy assessment will serve to quantify the uncertainty in the absolute position of the GCPs, identified on the panoramic images in the absence of artificial targets. Executed experiments showed that in tested UAVs, the choice of the GCPs has significant impact on point cloud accuracy. Estimated absolute accuracy of point clouds collected during both test flights was better than 5 cm.