Within the frame of the EFTTRA (Experimental Feasibility of Targets for TRAnsmutation) cooperation, rods of 99Tc metal are irradiated in the Petten High Flux Reactor for 193 effective full power days, during which ~6% of the 99Tc is transmuted to the stable 100Ru. The radial and axial ruthenium distributions in one of the rods are measured by electron probe microanalysis. In the radial direction, the ruthenium concentration strongly increases in the outer rim of the sample, while the axial distribution shows little variation. The average ruthenium concentration, as measured by isotope dilution mass spectrometry, is (6.4 ± 0.2)% at 5 mm from the bottom of the rod and (6.1 ± 0.2)% at 5 mm from the top. The ruthenium concentrations calculated by the KENO three-dimensional Monte Carlo code, 6.1% at 5 mm from the bottom of the rod and 5.7% at 5 mm from the top, are in reasonable agreement with the measured ones. However, the calculated radial distribution of the ruthenium concentration does not agree with the measurements. The radial profile calculated by the MCNP Monte Carlo code, which uses a pointwise cross-section library, agrees much better with the measurements.