Equivalent spin-valves grown on silicon oxide (SiOx) substrates produced either by thermal oxidation of Si(100) wafers or low-pressure chemical vapour deposition (LPCVD) of the oxide have been studied by x-ray scattering, atomic force microscopy (AFM) and magnetotransport measurements. Grazing incidence x-ray scattering (GIXS) measurements have also been made on the bare substrates. The x-ray measurements, supported by AFM images, show a large difference not only between the roughness of the two substrate types but also of the spin-valves deposited on them. A high degree of conformality is observed in the roughness of the spin-valves. Magnetoresistance (MR) measurements made on the spin-valves show that the switching point of the sample grown on the LPCVD substrate is shifted away from the ideal zero point due to increased coupling and both the giant magnetoresistance (GMR) and exchange field are seen to fall with increasing roughness.