We have studied the structure and properties of palygorskite clays. A structure analysis was performed using two different models to reproduce the monoclinic and orthorhombic lattices, using the atomic positions and cell parameters of palygorskite structure suggested by several authors, we simulated structures using Molecular Dynamics and Quantum Mechanics. Modifications on the structure and elemental atom changes were made to obtain more stable configurations. X-ray diffraction patterns and high resolution electron microscopy images from simulated structures were compared with experimental results. It could be observed that orthorhombic model shows a better fitting than monoclinic models. These results might help to understand many of the properties of archaeological pigments, such as, Maya Blue, in which palygorskite clay was the main component.