Biorefineries are increasingly important commercial facilities for the production of biofuels, biopower and various biomaterials from biomass with potentials to displace several existing industries currently based on polluting and finite fossil resources. Biorefinery systems consist of biorefinery facilities and their entire value chain. Integration of biorefinery systems aims at optimising the use of energies and materials in the total chain from biomass plantations to end product utilisation and is therefore capable of successfully improving economic viability and sustainability of biorefineries. Total Chain Integration can minimise capital and operating expenditures, maximise the quality, quantity and value of biorefinery bioproducts as well as minimise environmental impacts and maximise societal benefits. In order to efficiently perform Total Chain Integration advanced holistic software tools dedicated to biorefinery systems need to be developed. This review study systematically analyses Total Chain Integration of sustainable biorefinery systems. Existing knowledge is systematised by characterising system boundaries, principles, and integration methodologies. Further, approaches used in integration of biorefinery systems are defined and their implementation is briefly illustrated by case studies. Finally, state-of-the-art software tools for biorefinery integration are analysed and the requirements of a software tool for Total Chain Integration are provided. The review findings show that in order to develop truly economically viable and sustainable biorefinery systems tight integration is required. Essential integration approaches include integration of platforms, exchanging wastes and products with other industries, applying more efficient conversion routes, effective ways of enlarging feedstocks base, providing ecosystem and social services, and optimising biomass supply chain. Total Chain Integration requires software tools accounting for technical, economic, environmental and societal optimisation objectives within all system boundaries and the whole life cycle. The requirements of such software are proposed. Software enhanced Total Chain Integration has a potential to successfully achieve economic viability and sustainability of biorefinery systems in the business practice. (C) 2016 Elsevier Ltd. All rights reserved.