P-glycoprotein actively transports a wide variety of chemically diverse compounds out of the cell. Based on a comparison of 100 compounds previously tested as P-glycoprotein substrates we suggest that a set of well-defined structural elements is required for an interaction with P-glycoprotein. The recognition elements are formed by 2 (type I unit) or 3 electron donor groups (type II unit) with a fixed spatial separation. Type I units consist of 2 electron donor groups with a spatial separation of 2.5 +/- 0.3 A. Type II units contain either 2 electron donor groups with a spatial separation of 4.6 +/- 0.6 A or 3 electron donor groups with a spatial separation of the outer 2 groups of 4.6 +/- 0.6 A. All molecules which contain at least 1 type I or 1 type II unit are predicted to be P-glycoprotein substrates. The binding to P-glycoprotein increases with the strength and the number of electron donor or hydrogen-bonding acceptor groups forming the type I and type II units. Correspondingly a high percentage of amino acids with hydrogen bonding donor side chains is found in the transmembrane sequences of P-glycoprotein relevant for substrate interaction. Molecules which minimally contain 1 type II unit are predicted to be inducers of P-glycoprotein overexpression.