This paper proposes a pose-based algorithm to solve the full SLAM problem for an Autonomous Underwater Vehicle (AUV), navigating in an unknown and possibly unstructured environment. The technique incorporate probabilistic scan matching with range scans gathered from a Mechanical Scanned Imaging Sonar (MSIS) and the robot dead-reckoning displacements estimated from a Doppler Velocity Log (DVL) and a Motion Reference Unit (MRU). The raw data from the sensors are processed and fused in-line. No priory structural information or initial pose are considered. The algorithm has been tested on an AUV guided along a 600m path within a marina environment, showing the viability of the proposed approach.