Doublesex (DSX) is a transcription factor that regulates sexual differentiation in Drosophila. Alternate splicing gives rise to male- and female-specific isoforms. A potent modulator of the yolk protein gene (yp), the male isoform (DSX^M) represses transcription of yp whereas the female isoform (DSX^F) is an activator. DSX contains two recognized domains, an N-terminal DNA-binding domain (shared between isoforms) and a C-terminal domain (CTD) that is responsible for oligomerization and presumably transcriptional regulation. The CTDs contain sex-specific C-terminal sequences with opposite gene-regulatory properties. Our work focuses on the structure and function of the novel DSX CTDs. The crystal structure of a core CTD dimerization domain was determined to a resolution of 1.6 Å using single-wavelength anomalous dispersion (SAD) phasing. The solution structure was independently determined using heteronuclear 3D/4D-NMR methods. The structure, similar in solution and in the crystal state, reveals a novel helical dimer with a disordered female-specific tail. Packing constraints in the dimer rationalize the intersexual phenotype of a variant fly containing a point mutation at the dimer interface. CD-detected GuHCl titrations indicate a remarkably stable dimer; the dimerization constant is ca. 0.1 nM. Dynamics, investigated through HX exchange experiments, indicate that the dimer interface defines a global hydrogen-exchange core. Integral to the function of DSX^F is the transcriptional coactivator Intersex (IX), homologous to a subunit of the mammalian Mediator complex. The IX-binding surface of the DSX^F domain has been mapped to specific grooves that span the sex-specific and non-sex-specific portions of the protein. The DSX structure may provide a foundation for genetic studies of female-specific courtship behavior in Drosophila.