The surface morphology of supported Pd/graphite film catalysts imaged by scanning tunneling microscopy (STM) shows that the microstructure is strongly dependent on the pretreatment and reaction conditions. Results obtained from the ultrahigh vacuum STM have validated the ambient STM images provided the film structures are sufficiently larger than 10 nm. Significant morphological changes occurring during reaction were accompanied by alteration in the activity and selectivity. Three Pd/HOPG films were prepared by exposure to different treatment conditions. It was found that the films with different microstructure exhibit different catalytic behavior, whereas the two films with similar structures prepared by different procedures have similar activity and selectivity.