The knowledge of physical and chemical properties of a compound is required for understanding and modeling the action of a compound in drug discovery, environmental chemistry, and other chemical industries. This chapter first provides an overview of typical methods for the prediction of physicochemical properties and gives a more detailed analysis of several physicochemical properties important for drug discovery and chemical industry in general. It then exemplifies the modeling of several properties, that is, octanol/water partition and distribution coefficients, water solubility, melting point (MP), pKa value, and thermochemical properties. Many physicochemical properties of compounds are strongly interconnected. The relationships between physicochemical properties can be derived based on a theoretical analysis or/and found empirically. The chapter helps the readers to derive quantitative relationships between a property and a structure, and also it summarizes the limitations of different modeling techniques.