This chapter outlines the progress made in analyzing and predicting binding pockets. Typical structurebased drug discovery project begins with 3D structure of the target protein, identifies putative binding pocket(s), analyses its properties and performs virtual screening to find suitable candidate drug molecules. The success crucially depends on both the correct binding pocket prediction and revealing essential biophysical characteristics of the binding site. These two tasks are intertwined, since many of the binding pocket prediction methods relay of previous studies on binding site physico-chemical properties. In this chapter the most popular methods and approaches for both analysis and prediction of binding sites are reviewed and the corresponding URLs are provided. The emerging picture is the most successful methods of binding site prediction are based on many components analysis and thus reflect the complex nature of the receptor-ligand interactions.