A new versatile and geometrically reconfigurable ultrasonic tomography system (UTS) has been designed to inspect and obtain information about the internal structure and inner damage of columns in heritage buildings. This nondestructive system is considered innovative because it aims to overcome common limitations of existing systems. Tomographic inspections are typically carried out manually and are thus limited to small portions of construction elements. The proposed UTS allows the automatization of the inspection and the generation of numerous tomographic slices along the height of the column. It is valid for multiple types of columns and materials. In the present work, the system was tested on two limestone columns of the north façade of the Convent of Carmo in Lisbon, Portugal. The UTS is composed of a mechanical and an electronic system. The mechanical system consists of four linear motion subsystems mounted in a square setup. A transducer is placed on each of the axes, acting as emitter or receiver of the ultrasonic signals. The mechanical system also includes a guide system to adapt the inspections to the complex geometry of the columns. The electronic system allows the control and the synchronization of the movements and the emission/reception configuration of the four ultrasonic transducers.