In this protocol, we describe the application of commercially available three-dimensional organotypic tissues of human oral mucosa to study the interaction between Candida albicans and epithelial cells. Infection experiments show high reproducibility and can be used to analyse directly pathogen/epithelial cell interactions. However, the system is also very flexible. Using histological, biochemical, immunological, and molecular methods, it is possible to analyse several stages of infection by C. albicans wild type or mutant strains and demonstrate the consequence of disrupting genes encoding putative virulence factors required for host cell invasion and immune defence induction. This model provides information about host and pathogen protein and gene expression during direct interactions with each other. It can additionally be supplemented with other host factors, such as immune cells, saliva, and probiotic bacteria, which are relevant for host immune defence in the oral cavity.