Heat treatment of wood is an effective method to improve the dimensional stability and durability against biodegradation. Optimisation of a two-stage heat treatment process at relatively mild conditions (<200°C) and its effect on the anatomical structure of softwoods were investigated by means of a light and scanning electron microscopic analysis. Heat treatment did have an effect on the anatomical structure of wood, although this depends on the wood species considered and on the process method and conditions used. Softwood species with narrow annual rings and/or an abrupt transition from earlywood into latewood were sensitive to tangential cracks in the latewood section. Radial cracks occurred mainly in impermeable wood species such as Norway spruce, caused by large stresses in the wood structure during treatment. Sapwood of treated pine species revealed some damage to parenchyma cells in the rays and epithelial cells around resin canals, whereas this phenomenon has not been noticed in the heartwood section. Treated radiata pine resulted in a very open and permeable wood structure limiting the applications of this species. Broken cell walls perpendicular to the fibre direction resulting in transverse ruptures have been noticed in treated softwood species. This contributes to abrupt fractures of treated wood as observed in bending tests which can lead to considerably different failure behavior after impact or mechanical stress. In some treated softwood species maceration (small cracks between tracheids) was noticed after heat treatment. Heat treatment did not cause damage to the ray parenchyma pit membranes, bordered pits and large window pit membranes; the margo fibrils appeared without damage. Compared to the other softwood timbers tested European grown Douglas fir was the timber that stands heat treatment the best