Mapping with Micro Aerial Vehicles (MAVs whose weight does not exceed 5 kg) is gaining importance in applications, such as corridor mapping, road and pipeline inspections, or mapping of large areas with homogeneous surface structure, e.g. forest or agricultural fields. When cm-level accuracy is required, the classical approach of sensor orientation does not deliver satisfactory results unless a large number of ground control points (GCPs) is regularly distributed in the mapped area. This may not be a feasible method either due to the associated costs or terrain inaccessibility. This thesis addresses such issues by presenting a development of MAV platforms with navigation and imaging sensors that are able to perform integrated sensor orientation (ISO). This method combines image measurements with GNSS or GNSS/IMU (Global Navigation Satellite System/Inertial Measurement Unit) observations. This innovative approach allows mapping with cm-level accuracy without the support of GCPs, even in geometrically challenging scenarios, such as corridors. The presented solution also helps in situations where automatic image observations cannot be generated, e.g. over water, sand, or other surfaces with low variations of texture. The application of ISO to MAV photogrammetry is a novel solution and its implementation brings new engineering and research challenges due to a limited payload capacity and quality of employed sensors on-board. These challenges are addressed using traditional as well as novel methods of treating observations within the developed processing software. The capability of the constructed MAV platforms and processing tools is tested in real mapping scenarios. It is empirically confirmed that accurate aerial control combined with a state-of-the-art calibration and processing can deliver cm-level ground accuracy, even in the most demanding projects. This thesis also presents an innovative way of mission planning in challenging environments. Indeed, a thorough pre-flight analysis is important not only for obtaining satisfactory mapping quality, but photogrammetric missions must be carried out in compliance with state regulations.