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Waveguide based 1-D photonic crystal (PC) microcavities in silicon-on-insulator are investigated by 2-D finite-difference time-domain method. Values up to 6.7 times106 for the quality factor (Q) are feasible if the cavities are properly designed. The factors that govern Q are analyzed in both real space and momentum space. Etching down into the SiO2 layer is found to give more than 20% improvement in Q compared to the structure in which etching is stopped at the oxide layer. Short air gap mirrors are used to reduce the vertical scattering loss. The addition to the Bragg mirrors of tapered periods optimized to produce a cavity mode with a near Gaussian shaped envelope results in a major reduction in vertical loss. A new tapered structure with varying Si block width demonstrates an ultrahigh-Q and relieves the fabrication constraints compared to the conventional air slots tapered structure.