The ability of Gold software to predict the binding disposition of carbonic anhydrase (CA) inhibitors was evaluated using CA II as a case study. The best procedure was subsequently used for docking almost 300 CA II ligands, and the best poses were used as an alignment tool for the development of a 3D quantitative structure-activity relationship (QSAR) study. Evaluation of the resulting 3D-QSAR model allowed us to indicate the ligand properties and residues important for CA II inhibition. Since CAs are an important target involved in many pathologies such as glaucoma, obesity, and tumors, the results obtained could accurately predict the binding affinity of newly designed CA II inhibitors. Furthermore, it is reasonable that this strategy could be profitably used also for the investigation of other CAs.