Orthodontic aligners 3D-printed in resin currently provide a viable alternative to thermoformed ones. However, concerns have been raised regarding their biocompatibility. This review addressed the available scientific evidence on the biological properties of marketed resins for 3D printing of orthodontic aligners, encompassing cytotoxicity, estrogenicity, biofilm formation, and oral soft tissues reactions. A comprehensive literature search of several databases was conducted and PRISMA guidelines were followed to summarize the retrieval. Eleven studies were included in the review. They provided information on only three marketed resins: Tera Harz TC-85 DAC and Tera Harz TA-28 (Graphy) and Clear-A (Senertek). For the last two materials, only one investigation has been performed. Despite the large variability in experimental protocols, the lack of cytotoxicity of Tera Harz TC-85 DAC was a consistent finding. Also, no estrogenic effect was detected for this resin, in line with the lack of any bis-phenol A precursor in its chemical composition. In two clinical studies, oral soft tissue reactions were reported as rare and non-serious occurrences. Biofilm adhesion was regarded as critical for the clinical safety of 3D-printed aligners. Standardization of in vitro protocols, also including more clinically relevant settings, chemical characterization of the resins' eluates, and collection of additional in vivo data are advised to improve the quality of the evidence.