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Vaginal drug delivery systems are often preferred for treating a variety of diseases and conditions of the female reproductive tract (FRT), as delivery can be more targeted with less systemic side effects. However, there are many anatomical and biological barriers to effective treatment via the vaginal route. Further, biocompatibility with the local tissue and microbial microenvironment is desired. A variety of in vitro and ex vivo models are described herein for evaluating the physicochemical properties and toxicity profile of vaginal drug delivery systems. Deciding whether to utilize organoids in vitro or fresh human cervicovaginal mucus ex vivo requires careful consideration of the intended use and the formulation characteristics. Optimally, in vitro and ex vivo experimentation will inform or predict in vivo performance, and examples are given that describe utilization of a range of methods from in vitro to in vivo. Lastly, we highlight more advanced model systems for other mucosa as inspiration for the future in model development for the FRT.