Thin films of BaZr1-xScxO3-x/2, (0 ≤ x ≤ 0.64), well known as proton conducting solid electrolytes for intermediatetemperature solid oxide fuel cell, were deposited by magnetron sputtering. X-ray diffraction analysis of theas deposited films reveals the presence of single-phase perovskite structure. The films were deposited on fourdifferent substrates (c-Al2O3, LaAlO3〈100〉, LaAlO3〈110〉, LaAlO3〈111〉) yielding random, (110)- or (100)-orientedfilms. The stability of the as-deposited films was assessed by annealing in air at 600 ◦C for 2 h. Theannealing treatment revealed instabilities of the perovskite structure for the (110) and randomly oriented films,but not for (100) oriented film. The instability of the coating under heat treatment was attributed to the lowoxygen content in the film (understoichiometry) prior annealing combined with the surface energy and atomiclayers stacking along the growth direction. An understoichiometric (100) oriented perovskite films showedhigher stability of the structure under an annealing in air at 600 ◦C.