There are many works and interests focused on the development of optical sensors based on porous anodic aluminum oxide membranes (AAO). Normal incidence birefringence (BR) is present in AAO when is obtained from a monocrystalline aluminum substrate but his effect has been largely ignored since it is canceled out in a poly-crystalline substrate. Nevertheless, this averaging of BR limits the optical performance of AAO membranes in optical devices. In this work, we study normal incidence BR in AAO for different crystal orientations of the aluminium substrate using a polycrystalline substrate and a simple thermo-mechanical treatment to obtain millimeter size crystalline regions. We found that normal incidence BR is minimum at [100] and [111] orientations and reaches a maximum of ∼ 1.8 ⋅ 10−3 at intermediate orientations. In this case, the BR can be associated with a slight deformation of the structure perpendicular to the direction of the pores, confirmed through scanning electron microscope images. Furthermore, we propose a simple model of elliptical section pores that quantitatively explain the origin of normal incidence BR in AAO. Considering the effect of BR, the design of sensors could be improved to obtain higher quality factors or to incorporate new optical functionalities to these already versatile membranes.