Church towers are key cultural heritage. In theory, towers are vertical, while facade elements are symmetrically positioned around the tower axis. However, during service of a structure, building and lifetime conditions cause deviations, with associated risks. Laser scanning point clouds can be used to assess the structural state but a universal approach was missing. The proposed algorithm first estimates the tower inclination, and tests which multi-axis representation best represents the course of the tower. Next, point cloud spatial expansion recovers relative distances and deviations of facade elements. The resulting procedure was applied to assess two Dutch medieval towers including the Old Church in Delft and the St. Bavo Church in Haarlem, respectively. As results of analysis, significant asymmetry was found with a 1.4° deviation of the multi-modal axis of the St. Bavo Church tower together with variations of 0.1%–1.5% for facade slopes, while 0.1°–3.1° radial deviations were found in the position of the turrets of the Old Church tower.