Axin, Ccd1 (coiled-coil-DIX1), and Dishevelled (Dvl or Dsh) are three known DIX domain proteins that play important roles in Wnt signaling. In addition, Dvl and Axin can activate the MAP kinase JNK via distinct mechanisms, through interaction with MEKK1/4 and Rac GTPase, respectively. Axin utilizes two distinct domains for interaction with MEKK1 and MEKK4. Whereas JNK activation by Axin is regulated by several factors in the Wnt pathway, little is known about cross-regulation of Dvl-mediated JNK activation. In the present study, we have investigated if Ccd1 could play a regulatory role in Axin- and Dvl-mediated JNK activation. Here we show that Ccd1 drastically inhibited JNK activation both by Axin and by Dvl. Although DIX domains are sufficient for dimer formation between Dvl and Ccd1, Ccd1 also required its coiled-coil domain for inhibition of JNK activation by Dvl. Interestingly, Rac remained associated with Dvl heterodimerized with Ccd1. How Ccd1 blocks Rac/Dvl signaling to JNK is unclear. In contrast, Axin, when complexed with Ccd1, did not bind to MEKK1. Furthermore, Ccd1 physically interacted with MEKK4 in their physiological concentrations, and prevented MEKK4 from binding to Axin. Reduction of Ccd1 protein by siRNA could elevate JNK signaling as assayed with an AP1-dependent transcriptional reporter. We have therefore demonstrated that Ccd1 inhibits Axin-mediated JNK activation by simultaneously adopting two distinct mechanisms, one through conformational changes that disallow MEKK1 binding, and the other via direct sequestration of MEKK4.