Several models (cluster, periodic, and hybrid) and methods of the description of properties of transition metal ions in zeolites are reviewed and their reliability is discussed. It is concluded that the combined quantum mechanics / interatomic potential function (QM-Pot) technique is a suitable approach to the description of transition metal/zeolite systems. This method was used for the study of properties of copper ions in ZSM-5 and ferrierite matrices. The interactions of CO and NO with copper ions in both zeolites were investigated. The computational results offer interpretation of some experimental data at the atomic scale level.