Ovarian cancer stem cells (OCSCs) are in a transitional phase between epithelial and mesenchymal cell stages. Consequently, OCSCs possess a high degree of plasticity that complicates their identification and characterization. However, we recently demonstrated that the combined assessment of key antigens associated with cancer stem cells and the epithelial-mesenchymal transition can distinguish the phenotype of OCSCs from more differentiated cells. In this chapter we describe in detail an appropriate sample preparation for the analysis of epithelial, mesenchymal, and cancer stem cell markers by flow cytometry and immunohistochemistry in ovarian cancer. Furthermore, we provide methods for the establishment of primary ovarian cancer cultures from solid tumors.