Cylindrical dielectric and semiconducting microdisks are becoming attractive for use as electromagnetic resonators for optical and terahertz-frequency devices. The effects of the substrate and the support pedestal on microdisk performance, however, are not well understood due to limitations of conventional analytical techniques. We present a study of the influence of the support structure, namely, the substrate and pedestal, on microdisk resonator performance using the finite-difference time-domain method. The field distributions, resonant frequencies, and Q factors of the microdisk are computed at various distances from the substrate and for different pedestal sizes. Results show that the supporting structure can significantly distort the field distribution in the disk, and therefore have significant effects on both resonant frequency and Q factor, which are major parameters in microdisk design.