The molecular packing of a new class of perylene diimide-based acceptor-donor (A-D) co-oligomers has been investigated by combining electron diffraction and X-ray scattering methods for AD dyads and an ADA triad structure. The AD and ADA compounds form highly ordered lamellar mesophases with well-defined donor and acceptor domains. To determine the structure of the co-oligomers, highly oriented films with different orientations were prepared. Both flat-on and edge-on orientations of the lamellae were obtained by using two different alignment methods. High temperature rubbing leads to edge-on oriented lamellae with the long molecular axis of the co-oligomer oriented almost parallel to the rubbing direction. Instead, on oriented substrates of poly(tetrafluoroethylene) (PTFE), flat-on lying lamellae with the pi-stacking direction oriented parallel to the PTFE chains are obtained. The structural data gathered by low dose selected area electron diffraction and high resolution transmission electron microscopy are used to establish a structural model of an AD dyad. Driven by the strong pi-stacking of the PDI core, both AD and ADA co-oligomers form two similar self-assembled lamellar structures with an original zipper-like organization of the PDI blocks.