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Thermal stresses generated by differences in the thermal expansion coefficients of InP and GaAs are analyzed in an attempt to introduce an InP-based light emitter into GaAs-based three-dimensional photonic crystal. Observations of the GaAs/InGaAsP bonding interface by scanning acoustic microscopy reveal that debonding occurs at approximately 300 °C due to thermal stress. Calculations of thermal stress by a two-dimensional finite element method suggested that thermal stress could be reduced by thinning the substrate, which was confirmed experimentally. Using these results, a three-dimensional photonic crystal with light emitter was successfully fabricated. © 2003 American Institute of Physics.