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Thermal conductivities (k) of the individual layers of a GaN-based light emitting diode (LED) were measured along  using the 3-omega method from 100-400 K. Base layers of AlN, GaN, and InGaN, grown by organometallic vapor phase epitaxy on SiC, have effective k much lower than bulk values. The 100 nm thick AlN layer has k = 0.93 ± 0.16 W/mK at 300 K, which is suppressed >100 times relative to bulk AlN. Transmission electron microscope images revealed high dislocation densities (4 × 1010 cm-2) within AlN and a severely defective AlN-SiC interface that cause additional phonon scattering. Resultant thermal resistances degrade LED performance and lifetime making layer-by-layer k, a critical design metric for LEDs.