Zebrafish ovarian follicles are mainly composed of the oocyte and a thin layer of follicle cells. Recent studies have demonstrated extensive cell-cell interactions between the oocyte and surrounding follicle layer and that the two compartments communicate mostly through paracrine factors. To understand the paracrine communication within the follicle, it is essential to know the spatial expression patterns of genes in the two compartments. However, since the follicle layer is extremely thin and the oocytes are enormous in size in fish, it is often difficult to detect gene expression by traditional methods such as in situ hybridization. Separation of the oocyte and surrounding follicle layer followed by RT-PCR detection provides a sensitive way to reveal the expression of individual genes in the two compartments of the follicle. This chapter introduces a method for mechanic separation of the oocyte and follicle layer at full-grown stage for expression analysis. Since fish have similar follicle structure, this method may also be used in other species as well.