Biological activity and toxicity of molecules are the major aspects on understanding diverse bio-mechanisms in living systems. Estimation of degree of activity and toxicity of molecules in a target is very important for their control and applications. However, experimental determination of bio-activity or toxicity is a mammoth task due to cost, time and availability of resources. In this direction, a fruitful mathematical approach has been successfully developed as Quantitative Structure Activity Relationship (QSAR). A successful QSAR modeling can also predict the bio-activity and toxicity of unknown homologous compounds. The present book addresses details of QSAR methods and relevant statistical analysis, various structural descriptors along with a couple of case studies considering important role of nucleic acid bases during the interaction of bio-active/toxic molecules with biological targets. The bio-activity of a series of acyl-CoA: cholesterol O-acyltransferase (ACAT) inhibitors, viz. aminosulfonyl ureas and toxicity of a series of Polycyclic Aromatic Hydrocarbons (PAHs) are reported in light of their interaction with model bio-systems.