We present analysis of thermal stability of thin GdScO3 films grown on silicon and InAlN/GaN substrates. The GdScO3 films were prepared by liquid injection metal organic chemical vapor deposition at 600 °C. The films were processed after deposition by rapid thermal annealing in nitrogen ambient at 900, 1000 and 1100 °C during 10 s. In addition, annealing of the GdScO3 films on InAlN/GaN substrate at 700 °C during 3 hours was performed. The samples were analyzed by grazing incidence X-ray diffraction (GIXRD), X-ray reflectivity (XRR) and time-of-flight secondary ion mass spectroscopy (ToF SIMS). GIXRD confirmed that the as-deposited GdScO3 films were amorphous. Recrystallization of the films on both substrates occurred at 1100 °C. ToF SIMS depth profile of the films annealed at 1000 °C indicated strong reaction of the GdScO3 film with the Si substrate. For the InAlN/GaN substrate rapid thermal annealing at 900 °C induced diffusion of the In and Al atoms into the top GdScO3 layer. Thermal treatment at 700 °C for 3 hours presents upper limit of the acceptable thermal budget for the GdScO3/InAlN interface.