In high-precision 3D gel dosimetry, long MR measurement times together with a high amount of RF energy being absorbed by the phantom are very common, and result in a spatially dependent temperature rise in the gel. As T2 of the dosimeter gel is temperature dependent, dose estimation will be affected. In this study we assess the temperature rise in the dosimeter gel by use of MR temperature mapping and computer modelling. It is shown that in conventional MR sequences, where linear k-space sampling is used, a temperature rise of 3 °C results in a dose underestimation of 10% over the whole dose map. To correct for these dose errors, a compensation method involving centric k-space ordering is suggested. Computer simulations have been performed to analyse the robustness of the proposed method. Applying the compensated sequence, a temperature rise of 3 °C leads to a narrow dose artefact of the order of 3% for a 'worst case' situation in which a single pixel dose gradient is assumed. Negligible deviations are found in the cost of the dose map.