GaN/Si heterostructures were prepared by molecular beam epitaxy employing different Si substrate nitridation times from 0 to 60 min. The GaN/Si structural properties were evaluated by transmission electron microscopy, X-ray diffraction, and atomic force microscopy. Thermal properties of the GaN/Si heterostructures were studied by the photoacoustic technique. Employing a two-layer model the interfacial thermal conductivity (η) was obtained as a function of the nitridation time. η presented low values of around 150W/cm(2) K in samples with poor structural characteristics. We obtained the maximum value of η = 255W/cm(2) K for the sample prepared with the optimal nitridation time. The variation of the parameter η for different nitridation times can be associated to interface phonon scattering process by the presence of disorder at the GaN/Si interface. © 2005 Elsevier B.V. All rights reserved.