X-ray fluorescence microscopy (XFM) is a powerful tool for mapping and quantifying the spatial distribution of elemental composition of biological samples. Recently, it was reported that transition metal fluctuations occur during Drosophilareproduction, analogous to what is seen in mammals and nematodes, and may contribute to Drosophilafemale fertility. To further support XFM studies on Drosophilareproduction, we describe procedures for isolating oocytes and activated eggs and examining their elemental composition by XFM scanning and analysis.