The role of transition metals (TM) and their ions in the structure and function of many biologically important systems is fundamental and the metals are indispensable. Therefore, it is challenging to explain the underlying concepts with the tools of quantum chemistry. In this article, we present a concise review on the problems encountered in theoretical studies of TM systems and the methodology of their quantum-chemical calculations. Particularly, modern and popular density functional theory (DFT) methods are presented and discussed in more detail. Since most chemical and biochemical processes occur in the surrounding environment (e.g., solution, protein body), the techniques dealing with its incorporation into the quantum chemical calculation are mentioned as well. In the end, several quantum chemical programs are listed.