Mega-voltage computed tomography (MVCT) and kilo-voltage cone beam CT (CBCT) are routinely used in image-guided radiation therapy. In current practice, doses from MVCT and CBCT are reported with no correction for radiation quality. In this study, we compared microdosimetric properties as well as doses for MVCT and CBCT. Monte Carlo simulation codes BEAMnrc and DOSXYZnrc were used to simulate a Varian CBCT 125 kVp photon beam and primary electron spectra for CT sets of two patients. The revised Oak Ridge Electron transport Code (NOREC) was used to simulate electron tracks in liquid water. C++ code was developed to compute lineal energy in a sphere of 1 μm diameter. Dose-mean lineal energy-based quality factors were calculated for critical organs in-field. The estimated quality factor for CBCT is up to a factor of 1.3 times that of MV beams.