Density functional theory method has been employed to investigate the structures of the prototypical technetium-labeled diphosphonate complex 99mTc-MDP, where MDP represents methylenediphosphonic acid. A total of 14 trial structures were generated by allowing for the geometric, conformational, charge, and spin isomerism. Based on the optimized structures and calculated energies at the B3LYP/LANL2DZ level, two stable isomers were determined for the title complex. And they were further studied systematically in comparison with the experimental structure. The basis sets 6-31G*(LANL2DZ for Tc), 6-31G*(cc-pVDZ-pp for Tc), and DGDZVP have also been employed in combination with the B3LYP functional to study the basis set effect on the geometries of isomers. The optimized structures agree well with the available experimental data, and the bond lengths are more sensitive to the basis set than the bond angles. The charge distributions were studied by the Mulliken population analysis and natural bond orbital analysis. The results reflect a significant ligand-to-metal electron donation.