We developed a simple model to investigate the effect of lipid clustering on the local interlayer distance in a cluster of interacting lamellae. The model, based on nonequilibrium thermodynamics and linear stability theories, explores the early stages of the lamella-lamella phase separation process where the lateral diffusion is much faster than the interlamellar lipid exchange. Results indicate, in the early stages, the presence of locally distorted regions with a higher concentration of one lipid component and an anomalous repeat distance. Experimental cases are presented, consisting of multi lamellar-oriented depositions of phospholipids containing minority amounts of ganglioside or sphingomyelin under a low-hydration condition. The minority components are known to form domains within the phospholipid bilayer matrix. The low water content inhibits the lipid exchange among nearby lamellae and strengthens lamella-lamella interaction, allowing for a straightforward comparison with the model. Small-angle and wide-angle neutron diffraction experiments were performed in order to detect interlayer distances and local chain order, respectively. Lamellar stacking splitting has been observed for the ganglioside-containing lamellae, induced by in-phase lipid clustering. In excess water and after long equilibration times, these local structures may further evolve, leading to coexisting lamellar phases with different lipid compositions and interlayer distances.