Organic polymers or crystals are commonly used in manufacturing of today's electronically functional devices (OLEDs, organic solar cells, etc). Understanding the morphology in general and at the interface in particular is of paramount importance. Proper knowledge of molecular orientation at interfaces is essential for predicting optoelectronic properties such as exciton diffusion length, charge carrier mobility and molecular quadrupole moments. Two promising candidates are pentacene and PTCDA. Different orientations of pentacene on PTCDA have been investigated using an atomistic molecular dynamics approach. Here, we show that the degree of disorder at the interface depends largely on the crystal orientation and that more ordered interfaces generally suffer from large vacancy formation.