Ceramides are particularly abundant in the stratum corneum lipid matrix, where they determine its unusual mesostructure, are involved in the lateral segregation of lipid domains in biological cell membranes, and are also known to act as signaling agents in cells. The importance attributed to ceramides in several biological processes has heightened in recent years, demanding a better understanding of their interaction with other membrane components, namely, cholesterol. Structural data concerning pure ceramides in water are relatively scarce, and this is even more the case for mixtures of ceramides with other lipids commonly associated with them in biological systems. We have derived the thermotropic binary phase diagram of mixtures of N-palmitoyl-D-erythro-sphingosine, C16:0-ceramide, and cholesterol in excess water, using differential scanning calorimetry and small- and wide-angle X-ray diffraction. These mixtures are self-organized in lamellar mesostructures that, between other particularities, show two ceramide to cholesterol crystalline phases with molar proportions that approach 2:3 and 1:3. The 2:3 phase crystallizes in a tetragonal arrangement with a lamellar repeat distance of 3.50 nm, which indicates an unusual lipid stacking, probably unilamellar. The uncommon mesostructures formed by ceramides with cholesterol should be considered in the rationalization of their singular structural role in biological systems.