Stacking faults are two-dimensional planar defects frequently arising in zeolites, modifying their properties and potentially affecting their performance in catalysis and separation applications. In classical zeolite intergrowths, a topologically unique zeolite layer may often pile up after some spatial transformation (lateral translation, rotation, and/or reflection) that may occur in different amounts or directions with about similar probabilities, leading to a difficult to control disorder. Here, we present a new kind of zeolite intergrowth that requires an additional topologically distinct layer rather than a spatial transformation of a unique one. Stacking of the so-called pentasil layers produces the well-known medium pore zeolite MFI. Intercalation in strict alternation of a topologically distinct second layer sandwiched between pentasil layers expands the structure to produce the new extra-large pore IDM-1. Stacking disorder modulates the structural expansion along the stacking direction. The disordered materials have been studied by simulation of the X-ray diffraction patterns using the program DIFFaX and by Cs-corrected high-resolution electron microscopy. We show that disorder does not occur at random but in extended domains and can be controlled all the way from MFI to IDM-1 by just varying the concentration of the synthesis mixture.