A hardwood, Eucalyptus globulus Labill., and a softwood Pinus pinaster Aiton., were heat treated at temperatures between 170 and 210ºC in an oven and in an autoclave. The samples were pre-extracted with dichloromethane, ethanol and water and ground prior to Fourier Transform Infrared (FTIR) spectroscopic analysis.The heat treatment caused significant changes in the chemical composition and structure of wood, in lignin and polysaccharides. Hemicelluloses were the first to degrade as proved by the initial decrease of the 1730 cm-1 peak due to the breaking of acetyl groups in xylan. Hardwood lignin changed more than softwood lignin, with a shift of maximum absorption from 1505 cm-1 to approximately 1512 cm-1 due to decrease of methoxyl groups, loss of syringyl units or breaking of aliphatic side-chains. The macromolecular structure becomes more condensed and there is a clear increase of non-conjugated (1740 cm-1) in relation to conjugated groups (1650 cm-1). However, the changes induced by the thermal treatment are difficult to monitor by FTIR spectroscopy due to the different chemical reactions occurring simultaneously.