Surface roughness was determined by x-ray diffraction for Ge films on Ge(001) grown by molecular beam epitaxy at room temperature. The truncation rod intensities and transverse-scan line profiles were measured as a function of perpendicular momentum transfer. Depending on the initial morphology of the surface, the same growth condition resulted in very different surface morphologies. Two types of initial surfaces were used. One was an atomically flat surface with very large terraces. The other, characterized by a roughness exponent α=1, had a high density of steps. Deposition on the flat surfaces resulted in a fairly smooth surface, but with a graded crystalline density below the surface. Deposition on the α=1 surfaces resulted in a more jagged surface characterized by an increase in the average height-height correlation function and a final roughness exponent of α-1/2. Additional and complementary information about the surface structure was obtained by scanning tunneling microscopy observations.