The DFF40-DFF45 heterodimeric complex is a primary player in apoptotic DNA fragmentation and is conserved among different species including Drosophila melanogaster. DFF40 is a novel nuclease, while DFF45 is an inhibitor that can suppress the nuclease activity of DFF40 via tight interaction. Unlike mammalian systems, apoptotic DNA fragmentation in the fly is controlled by four DFF-related proteins known as Drep1, Drep2, Drep3 and Drep4. Drep1 and Drep4 are DFF45 and DFF40 homologues, respectively. Although the exact functions of Drep2 and Drep3 are unclear, they are also involved in apoptotic DNA fragmentation via regulation of the function of Drep1 and Drep4. DFF-related proteins contain a conserved CIDE domain of ∼90 amino-acid residues that is involved in protein-protein interaction. In this study, the CIDE domains of Drep2 and Drep3 were purified in Escherichia coli, after which they formed a stable complex in vitro and were crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to a resolution of 5.8 Å.