This protocol describes the setup, maintenance and characteristics of models of epithelial Candida infections based on well-established three-dimensional organotypic tissues of human oral and vaginal mucosa. Infection experiments are highly reproducible and can be used for the direct analysis of pathogen-epithelial cell interactions. This allows detailed investigations of Candida albicans wild type or mutant strain interaction with epithelial tissue or the evaluation of the host immune response using histological, biochemical and molecular methods. As such, the models can be utilized as a tool to investigate cellular interactions or protein and gene expression that are not complicated by non-epithelial factors. To study the impact of innate immunity or the antifungal activity of natural and non-natural compounds, the mucosal infection models can be supplemented with immune cells, antimicrobial agents or probiotic bacteria. The model requires at least 3 days to be established and can be maintained thereafter for 2-4 days.