The thermal conductivity of AlN and SiC thin films sputtered on silicon substrates is measured employing the 3ω method. The thickness of the AlN sample is varied in the range from 200 to 2000 nm to analyze the size effect. The SiC thin films are prepared at two different temperatures, 20 and 500°C, and the effect of deposition temperature on thermal conductivity is examined. The results reveal that the thermal conductivity of the thin films is significantly smaller than that of the same material in bulk form. The thermal conductivity of the AlN thin film is strongly dependent on the film thickness. For the case of SiC thin films, however, increased deposition temperature results in negligible change in the thermal conductivity as the temperature is below the critical temperature for crystallization. To explain the thermal conduction in the thin films, the thermal conductivity and microstructure are compared using x-ray diffraction patterns.