In situ analysis of hydrocarbon desorption from hydrogen terminated Si(100) surfaces was performed in a silicon molecular beam epitaxy system, using reflection electron energy loss spectroscopy, in conjunction with conventional reflection high energy electron diffraction analysis. Measurements of C K edge core loss intensities demonstrate that this method is sufficiently sensitive to enable in situ analysis of hydrocarbon desorption at fractional monolayer coverages during low-temperature isothermal anneals. Hydrocarbon desorption was found to begin at 115 °C, and at 200 °C complete desorption occurred within 10 min. Hydrocarbon coverage was not measurably affected by operation of ionization gauge filaments during low temperature anneals, but was increased by transient outgassing of the sample holder, and its environs.