Although great efforts have been made to improve the physical anthropomorphic phantoms used to calibrate in vivo measurement systems, each of these phantoms represents a single average counting geometry and usually contains a uniform distribution of a radionuclide in the tissue substitute. As a matter of fact, significant corrections must be made to phantom-based calibration factors in order to obtain absolute calibration efficiencies applicable to a given individual. The OEDIPE software has been developed at the Institute for Radiological Protection and Nuclear Safety. It allows the direct and fast construction of a voxel phantom from medical images with a realistic distribution of activity between organs and its conversion into computer files to be used online for Monte Carlo calculations. OEDIPE allows determining and visualizing the variation of activity retention in the segmented organs of the phantom and running MCNPX with these calculated source-organs at different times after intake. The influence of the biokinetics of radionuclides on the in vivo measurement as well as the uncertainty on the estimated activity is quantified by comparing the numerical calibration coefficients obtained by considering realistic and dynamic biokinetic distributions of activity with the counting efficiency commonly obtained from simple, homogeneous, and static activity distributions in organs or in the whole body. As an application, the effect of long-term retention tissues was studied through a case of inhalation of an insoluble compound where the thoracic lymph nodes make a significant contribution to the lung counting efficiency. Future work will concern contamination through other routes of intake, such as a wound, and mixtures of radionuclides.