Analysis of electrostatic hydration free energies of the isomers of the 99mTc-BAT and 99mTc-DADT complexes is carried out using the computer simulation technique. The results show that not only a correlation exists between the logarithm of the brain uptake and the electrostatic hydration free energy for the isomers of 99mTc-brain radiopharmaceu-ticals, but also a linear relationship exists between the logarithm of the ratio of the brain uptake of the syn isomer to that of the anti one and the difference between the electrostatic hydration free energy of the syn-isomer and that of the anti one. Furthermore, the investigation on the important factors influencing the brain uptakes of 99mTc-radiophar-maceuticals and the reasons of the different biodistribution of the isomers of the 99mTc-complexes is explored at the molecular level. The results may provide a reference for the rational drug design of brain imaging agents. Analysis of electrostatic hydration free energies of the isomers of the 99mTc-BAT and 99mTc-DADT complexes is carried out using the computer simulation technique. The results show that not only a correlation exists between the logarithm of the brain uptake and the electrostatic hydration free energy for the isomers of 99mTc-brain radiopharmaceu-ticals, but also a linear relationship exists between the logarithm of the ratio of the brain uptake of the syn isomer to that of the anti one and the difference between the electrostatic hydration free energy of the syn- isomer and that of the anti one. Furthermore, the investigation on the important factors influencing the brain uptakes of 99mTc-radiophar-maceuticals and the reasons of the different biodistribution of the isomers of the 99mTc-complexes is explored at the molecular level. The results may provide a reference for the rational drug design of brain imaging agents.