BACKGROUND: Biomass is the only renewable feedstock containing carbon, and therefore the only alternative to fossil-derived crude oil derivatives. However, the main problems concerning the application of biomass for biofuels and bio-based chemicals are related to transport and handling, the limited scale of the conversion process and the competition with the food industry. To overcome such problems, an integral processing route for the conversion of (non-feed) biomass (residues) to transportation fuels is proposed. It includes a pretreatment process by fast pyrolysis, followed by upgrading to produce a crude-oil-like product, and finally co-refining in traditional refineries. RESULTS: This paper contributes to the understanding of pyrolysis oil upgrading. The processes include a thermal treatment step and/or direct hydroprocessing. At temperatures up to 250 degrees C (in the presence of H-2 and catalyst) parallel reactions take place including re-polymerization (water production), decarboxylation (limited CO2 production) and hydrotreating. Water is produced in small quantities (approx. 10% extra), likely caused by repolymerization. This repolymerization takes place faster (order of minutes) than the hydrotreating reactions (order of tens of minutes, hours). CONCLUSIONS: In hydroprocessing of bio-oils, a pathway is followed by which pyrolysis oils are further polymerized if H-2 and/or catalyst is absent, eventually to char components, or, with H-2/catalyst, to stabilized components that can be further upgraded. Results of the experiments suggest that specifically the cellulose-derived fraction of the oil needs to be transformed first, preferably into alcohols in a 'mild hydrogenation' step. This subsequently allows further dehydration and hydrogenation. (C) 2010 Society of Chemical Industry