Light detection and ranging (LiDAR) has demonstrated its capabilities as a prominent technique for the direct acquisition of high density and accurate topographic information. To achieve the potential accuracy of such systems, a rigorous system calibration should be performed. We introduce a novel rigorous LiDAR system calibration procedure where the system parameters are determined by minimizing the discrepancies among conjugate surface elements in overlapping strips and control data, if available. The method is automated and does not require specific features (e.g., planes or lines) in the covered area or preclassification of the point cloud. Suitable primitives, which do not involve preprocessing of the data, are implemented. The correspondence between conjugate primitives is determined using a robust matching procedure. A modification to the Gauss Markov model is introduced to keep the implementation of the calibration procedure simple while utilizing higher order primitives. Experimental results have demonstrated the effectiveness of the proposed method over different types of terrain coverage. (C) 2012 Society of Photo-Optical Instrumentation Engineers (SPIE). [DOI: 10.1117/1.OE.51.7.076201]