PURPOSE: The validity of effective dose (ED) in medical applications, which mostly involving partial-organ irradiation, has long been argued. We now propose a new algorithm of effective dose evaluation for medical radiation exposure. The new algorithm will include new Relative Volume Factors, or RVFs, to account for the relative irradiated volume of the partially-irradiated organs, such as skin and bone marrow. METHODS: To validate the proposed algorithm, three ED evaluation methods were applied to five neuro-imaging protocols of a C-arm cone-beam CT: 1) MOSFET-anthropomorphic- phantom measurement for organ doses, ED evaluated with the original ICRP algorithm; 2) using the same MOSFET-measured organ doses, ED evaluated with the new algorithm; and 3) Monte Carlo (PCXMC, developed by STUK) dose estimation as gold standard. RESULTS: For all five imaging protocols, the ED evaluations by the new algorithm agreed very well with the Monte Carlo simulation results (within 10% difference), whereas the original ICRP algorithm overestimated EDs by approximately a factor of 2. CONCLUSIONS: The proposed algorithm provides a more accurate estimation of ED in medical exposures than the original ICRP algorithm. It potentially establishes the ED as a more reasonable index for cross-protocol dose comparison.