Soybean, an important source of food proteins, has received increasing interest from the public because of its reported health benefits. These health benefits are attributed to its components which include isoflavones, saponins, proteins and peptides. Lunasin, Bowman-Birk inhibitor, Kunitz trypsin inhibitor and β-conglycinin are some of the biologically active peptides and proteins found in soybean. This chapter provides a comprehensive review on the biological properties and the recently used techniques in the analysis and characterization of soy bioactive peptides. Also, the basic chemistry of each of the bioactive peptides is discussed. In sum, bioactive peptides can be accurately identified and quantified using different techniques and conditions which are important in order to accurately characterize their individual biological activities.