The quality of pentacene films in pentacene-based devices significantly affects their performance. In this report, the effects of various defects in graphene on a pentacene film were studied with scanning tunneling microscopy. The two most common defects found in the epitaxial graphene grown on SiC(0 0 0 1) substrates were subsurface carbon nanotube (CNT) defects and step edges. The most significant perturbation of the pentacene films was induced by step edges between single-layer and bilayer graphene domains, while the effect of step edges between single-layer domains was marginal. The subsurface CNT defects slightly distorted the structure of the single-layer pentacene, but the influence of such defects decreased as the thickness of the pentacene film increased. These results suggest that the uniformity of the graphene layer is the most important parameter in the growth of high-quality pentacene films on graphene.