In the search for new proteinase inhibitors we have focused on the screening and Computer Assisted Drug Design (CADD) studies of polyphenolic compounds. In this paper we report CADD of flavonoles and flavones as trypsin inhibitors concomitant by the screening results. 5,7-Dihydroxy flavonoid have been found to be a perspective trypsin/trypsin-like-enzyme inhibitor. Flavanones and isoflavones are less effective trypsin inhibitors due to a lost of the optimal geometry leading to hydrogen bond interactions. Four different interaction modes were observed, flavonoids are stabilised in S(1) region of beta-trypsin by formation of two (apigenin) or at least one hydrogen bond and other significant electrostatic interactions. Quercetin, myricetin and morin have shown to be the best trypsin inhibitors tested. In general, flavonoids with suitably located hydroxy groups and planar conformation are the building blocks able to replace guanidinobenzoyl part of successful inhibitors. Physiological nature of flavonoids reveals biotechnological source of new trypsin inhibitors as antipancreatitis, anticancer and anti-inflammation drugs.