The dependence on substrate temperature of the structural properties of Co thin films deposited on silicon substrates by RF magnetron sputtering with multipolar magnetic plasma confinement (MMPC) was investigated. The structure of the Co films was characterized by X-ray diffraction (XRD), and their surface morphology by atomic force microscopy (AFM). It was found that the surface morphology depended strongly on the substrate temperature. The surface of Co thin films deposited at 400°C exhibited round connected textures with a maximum Rq (root mean square roughness) of 5.48 nm, while the films deposited at room temperature exhibited salient connected textures with an Rq of less than 1.18 nm. Furthermore, the XRD spectrum intensity observed for the Co films deposited at 400°C was higher than that of the films deposited at room temperature.