Synchrotron x-ray diffraction reciprocal space mapping was performed on perfluoropentacene (PFP) thin films on SiO2 in order to determine the crystal structure of a novel, substrate-induced thin film phase to be monoclinic with unit cell parameters of a = 15.76 +/- 0.02 angstrom, b = 4.51 +/- 0.02 angstrom, c = 11.48 +/- 0.02 angstrom, and beta = 90.4 +/- 0.1 degrees. Moreover, layered and co-deposited heterostructures of PFP and pentacene (P) were investigated by specular and grazing-incidence x-ray diffraction, atomic force microscopy, and Fourier-transform infrared spectroscopy. For a ca. three-monolayers-thick PFP film grown on a P underlayer, slightly increased lattice spacing was found. In contrast, co-deposited P/PFP films form a new mixed-crystal structure with no detectable degree of phase separation. These results highlight the structural complexity of these technically relevant molecular heterojunctions for use in organic electronics.