The Vall d’Aran is located on the north face of the Spanish Pyrenees. There, we can find a unique ensemble of Romanesque churches built during the twelfth century, which have suffered large geometric deformations. Puig i Cadafalch (1908) pointed out that the basilica floor plan churches were initially covered with timber-frame roofs that transferred the weight vertically and were later substituted with barrel vaults supported on non-monolithic circular-section masonry columns. These columns have plumbed out through time, and the severity of the deformations is very conditioned by the sternotomy of the pieces, the general measures and the vaulted building system. The research analyses the geometric evolution of these churches, based on the quantification of their deformations in relation with the used construction system. The methodology is based on an exhaustive topographical campaign (2014–15) made with Terrestiral Laser Scanner. The study is conducted through sections from 3D models obtained from four different churches, from which the admissible mathematic-strain deformation will be studied. These churches have different construction phases and deformations that occurred over a period of six centuries, and they are prime study examples for this particular problem.