Secondary metabolites of Uruguayan native forest trees hold a great potential for new biomaterials applications in the national forest industry but remain poorly investigated. This work presents a synthesis of the main issues in identification, separation and chemical characterization of selected forest tree secondary metabolites as raw materials for innovative non-wood forest products, reached through an inter-institutional agreement between the National Agricultural Research Institute (INIA - Uruguay) and the Faculty of Chemistry of the Republic University of Uruguay. Based on research advances on domestication of native forest trees with high economic potential, executed since 2007, the activities focused on: (i) the bioprospection of three native tree species (ñandubay (Prosopis affinis Spreng.), algarrobo (Prosopis nigra Griseb.) and quillaja (Quillaja brasiliensis (St.Hil.) Mart.) and (ii) the identification and chemical characterization of selected secondary metabolites. In bioprospection, 31 individuals were sampled from a total of 200 candidate trees selected in P. affinis and P. nigra natural repartition area in the country and bark and wood chemical analysis were realized using HPLC methods. For Q. brasiliensis, more than 500 individuals were identified in its natural repartition area and protocols for leaves saponins extraction were designed .The results obtained until now encourage to continue investigations with selected secondary metabolites to support novel processes and products development and alternative biomaterials applications, promoting the use and management of forest native trees in Uruguay.