It is difficult to find research papers collecting comparative results about characterization studies of clear aligners. Therefore, the aim of this paper is to provide the first comparative analysis of most commercial clear aligners, in terms of their stability towards intra-oral staining agents, their physicochemical and optical properties, as well as their water absorption behavior. Five types of aligners, characterized by different techniques, are considered: Erkodur, Essix Plastic, Ghost Aligner, Zendura, and Invisalign. The obtained results show that clear aligners are made up of PETG, semi rigid PU, and a mixture of PU and PETG, with different degrees of crystallinity which affect the transparency of each aligner. In particular, the PETG-based materials reveal the highest value of short-range order and the highest properties in terms of transparency in the visible range. After 14 days of immersion into red wine and coffee, PETG and PU-based aligners reveal a perceivable change in color (NBS values from 1.5 to 3), corresponding to a loss of transparency due to the deposition of impurities on the surface. These results are particularly marked for Invisalign, showing changes towards other colors (NBS up to 35), probably due to the thermoforming process which led to the formation of a wrinkled surface entrapping the impurities.