The morphological, structural and spectroscopic properties of molecular double layers grown by organic molecular beam deposition have been investigated using atomic force microscopy, Nomarski microscopy, powder x-ray diffraction and electronic absorption spectroscopy. The structures, based on metal-free phthalocyanine (H2Pc), perylene-3, 4, 9, 10-tetracarboxylic dianhydride (PTCDA) and aluminum-tris-quinolate (Alq3), were deposited on glass substrates, with individual layer thicknesses ranging from 7 to 380 nm. Alq3 has no influence on the subsequent growth of either H2Pc or PTCDA, and its properties are not affected by a first molecular layer. By contrast, significant structural modifications are observed in double layers based on the two crystalline materials H2Pc and PTCDA. H2Pc deposited onto a PTCDA first layer departs from its herringbone structure, and adopts a layered structure with an interplanar spacing of 3.33 Å and an intermolecular shift of 1.7 Å. The structure of a PTCDA film deposited onto a α-H2Pc layer is completely disrupted. When PTCDA is deposited onto a β-H2Pc first layer, a morphological templating is observed and this annihilates any structural disruption. This is consistent with the growth of a microcrystalline PTCDA film on top of a α-H2Pc first layer. © 2002 American Institute of Physics.