The structural maintenance of chromosome (SMC) proteins are required for a number of essential nuclear processes, including those of chromosome condensation, chromatid cohesion, and DNA repair. Eukaryotic SMC proteins form heterodimers capable of binding DNA and possess a DNA-stimulated ATPase activity. They have a characteristic structure of terminal globular domains with two internal arms that are predicted to form a coiled-coil structure interspaced with a globular “hinge” domain. We report here that the predicted coiled-coil arms are disrupted at conserved sites in SMC proteins. These disruptions, which vary in length and sequence identity, abolish the otherwise symmetrical secondary structure of antiparallel SMC heterodimers and provide the first evidence for a possible functional orientation of eukaryotic SMC complexes. The retention of these breaks between evolutionarily distant, yet related, SMC members indicates that they may have a fundamental role in SMC heterodimer function.