Context. The Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) was designed to measure the composition of the gas in the coma of comet 67P/Churyumov-Gerasimenko, the target of the European Space Agency's Rosetta mission. In addition to the volatiles, ROSINA measured refractories sputtered off the comet by the interaction of solar wind protons with the surface of the comet. Aims. The origin of different solar system materials is still heavily debated. Isotopic ratios can be used to distinguish between different reservoirs and investigate processes occurring during the formation of the solar system. Methods. ROSINA consisted of two mass spectrometers and a pressure sensor. In the ROSINA Double Focusing Mass Spectrometer (DFMS), the neutral gas of cometary origin was ionized and then deflected in an electric and a magnetic field that separated the ions based on their mass-to-charge ratio. The DFMS had a high mass resolution, dynamic range, sensitivity that allowed detection of rare species and the known major volatiles. Results. We measured the relative abundance of all three stable silicon isotopes with the ROSINA instrument on board the Rosetta spacecraft. Furthermore, we measured 13C/12C in C2H4, C2H5, CO. The DFMS in situ measurements indicate that the average silicon isotopic composition shows depletion in the heavy isotopes 29Si and 30Si with respect to 28Si and solar abundances, while 13C to 12C is analytically indistinguishable from bulk planetary and meteorite compositions. Although the origin of the deficiency of the heavy silicon isotopes cannot be explained unambiguously, we discuss mechanisms that could have contributed to the measured depletion of the isotopes 29Si and 30Si. © 2017 ESO.