The crystalline and superconducting properties of sputtered a-axis oriented thin films of Y1Ba2Cu3O7-x on SrTiO3(100) and MgO(100) substrates are compared using X-ray diffraction (XRD), high-resolution electron microscopy (HREM), atomic force microscopy, critical current (J(c)) and surface resistance (R(s)) measurements. A two step self-template method was used for deposition, and HREM measurements revealed that the bulk film beyond the template was pure a-axis oriented on SrTiO3 and also on lattice-mismatched MgO. However, the nature of the template layer on the two substrates was completely different and the crystallinity of the film was found to be dependent on the crystallinity of the template. The J(c) and R(s) measurements indicated that the superconducting properties of the film on MgO owing to its poor crystallinity, were dominated by weak links in contrast to well-coupled grains for the film on SrTiO3.