A review, based mainly on own publications, is devoted to methods of investigation of “structure-bioavailability” relationships. The first part of this review contains information about classification of hydrogen bond descriptors, original 2D hydrogen bond thermodynamic descriptors, program HYBOT, original 3D hydrogen bonding potentials, original hydrogen bond surface area descriptors. The second part includes the results of applications of the above mentioned of hydrogen bond descriptors for prediction of bioavailability components such as lipophilicity, solubility in water and in physiological fluids, absorption and blood-brain barrier permeability.