In the present article we discuss the most recent data regarding the role of homocysteine, its cyclic thioester--homocysteine thiolactone and the process of protein N-homocysteinylation in human disease. The protective role of thiolactonase/paraoxonase enzyme, carried on high density lipoproteins (HDL) in human blood, as well as the influence of structural modifications on HDL function are discussed. We also describe the effect of vitamin therapy (folic acid, vitamins: B6, B12) used for lowering the homocysteine level in humans as well.