Conventional photon radiation therapy dose-calculation algorithms typically compute and report the absorbed dose to water (D(w)). Monte Carlo (MC) dose-calculation algorithms, however, generally compute and report the absorbed dose to the material (D(m)). As MC-calculation algorithms are being introduced into routine clinical usage, the question as to whether there is a clinically significant difference between D(w) and D(m) remains. The goal of the current study is to assess the differences between dose-volume indices for D(m) and D(w) MC-calculated IMRT plans. Ten head-and-neck (H&N) and ten prostate cancer patients were selected for this study. MC calculations were performed using an EGS4-based system. Converting D(m) to D(w) for MC-based calculations was accomplished as a post-MC calculation process. D(w) and D(m) results for target and critical structures were evaluated using the dose-volume-based indices. For H&N IMRT plans, systematic differences between dose-volume indices computed with D(w) and D(m) were up to 2.9% for the PTV prescription dose (D(98)), up to 5.8% for maximum (D(2)) dose to the PTV and up to 2.7% for the critical structure dose indices. For prostate IMRT plans, the systematic differences between D(w)- and D(m)-based computed indices were up to 3.5% for the prescription dose (D(98)) to the PTVs, up to 2.0% for the maximum (D(2)) dose to the PTVs and up to 8% for the femoral heads due to their higher water/bone mass stopping power ratio. This study showed that converting D(m) to D(w) in MC-calculated IMRT treatment plans introduces a systematic error in target and critical structure DVHs. In some cases, this systematic error may reach up to 5.8% for H&N and 8.0% for prostate cases when the hard-bone-containing structures such as femoral heads are present. Ignoring differences between D(m) and D(w) will result in systematic dose errors ranging from 0% to 8%.