The immune system is important to protect the host from fungal infections. Diverse cell types belonging to the innate or adaptive branch of the immune system act in a tightly coordinated and tissue-specific manner. Experimental mouse models of fungal infections have proved essential for assessing the protective principles against different fungal pathogens. Besides pathological, histological, biochemical and molecular parameters, the analysis of phenotypic and functional aspects of immune cells in infected tissues is key for understanding the mechanisms of antifungal defense. In this chapter, we describe a method based on flow cytometry to assess innate and adaptive immune cells isolated from an in vivo context in a qualitative and quantitative manner.