The radionuclide 99Mo has been prepared by 100Mo(γ, n) reaction using two types of natural molybdenum compound (molybdenum trioxide and zirconium molybdate gel) with the bremsstrahlung end-point energies of 10 and 15 MeV. After the equilibrium, 99mTc was separated as NaTcO4 from the irradiated samples using two different chemical procedures to examine the chemical yield. The separated Na[99mTc]TcO4 from the ZrMo gel has the 99Mo breakthrough of 99 % as well as chemical impurities of Al, Mo and Zr < 10 ppm. The estimation of 99Mo and 99mTc was done by using off-line γ-ray spectrometric technique. The chemical yield of the separated 99mTc from the dissolved molybdenum trioxide is 70.7–75.2 %, whereas in the undissolved zirconium molybdate gel, it is 19.1–43 %. The second method is preferable because it is user friendly in hospital radiopharmacy throughout the shelf-life.