Abstract: Analytical and high resolution electron microscopy have been used to study the effect of Zn- and Fe-doping on the micro structure of [001] YBa2Cu3O7-x thin films on [001] MgO substrates grown by magnetron sputtering. Special attention was paid to the presence of second phase inclusions and surface outgrowths such as CuO, Y2Ba1Cu1O5-x, Y2O3 in order to establish a relationship with the critical current density.