In this work we study the incorporation into dipalmitoylphosphatidylcholine (DPPC) small unilamellar vesicle (SUV), of three indols: Trp, indol-3 acetamide and N-acetyl tryptophan ethyl ester (NATE), and of three flavins: riboflavin (RF), lumiflavin (LF), and 2'3'4'5' riboflavin tetrapropionate (TPRF). The incorporation into the vesicle was determined by selective fluorescence quenching for the indols, and by equilibrium dialysis for the flavins. The more hydrophobic compound, the greater incorporation into the vesicle; therefore, TPRF and indol-3-acetamide and NATE are the flavins and indols, with the higher incorporation. Consequently, the higher efficiency for the indol photodegradation and the photoproducts generation was obtained when the hydrophobic compounds were irradiated with monochromatic light in the presence of the vesicle.