Production of bioethanol by lignocellulosics hydrolysis has a long history, and nowadays bioethanol application as transport fuel makes it a topical task worldwide. In all configurations of hydrolysis including moderns ones, a significant amount of a raw material (up to 40-45%) remains as a rich-in-lignin non-hydrolyzed residue (LHR), and the feasible use of this residue is the necessary condition for the cost-effective operation of bioethanol production. The large potential of LHR as the raw material for obtaining products useful for environment protection, agriculture and industry is good recognized. The aim of the present work was to study LHRs composition with emphasis on their lignin component chemical structure modification upon various stages of the bioethanol production process carried out in three different configurations: softwood acid hydrolysis (AH), separate enzymatic hydrolysis and fermentation (SHF), and simultaneous saccharification and fermentation (SSF) in pilot plant conditions in Sweden. The characterization of LHRs structure on molecular level was done applying Py-GC/MS. High portion of the carbohydrates-derived pyrolytic products for LHR samples after SHF and AH processes indicates on non-completeness of processing or development of side reactions and visa versa high portion of lignin-derived compounds – up to 80% (SSF) shows the efficiency of hydrolysis process. Using Py-GC/MS the changes in molecular structure of lignin component of non-hydrolyzed residues on various stages of the technological process of bioethanol production were revealed: development of condensation reactions, ether bonds cleavage, destruction of side propane chain, oxidation. The results of the present investigation allow to conclude that the application of Py-GC/MS opens the opportunity for prompt, detailed and reliable characterization of changes of the composition of ligno-carbohydrate complexes.