A comprehensive energy analysis software tool Tyndall Hydrogen Economy Scenario Investigation Suite (THESIS) has been developed for assessing the impact of major technological shifts in the provision of energy for integrated transport, electrical power, and heating/cooling applications. Historically, transport and electrical power have been treated as independent sectors, but, in the case where hydrogen fuel cells are extensively used in motive applications, complex inter-dependencies arise between the two (e.g., production of hydrogen by electrolysis of water, alternative use of hydrogen for electricity storage and subsequent regeneration). The THESIS model characterises a country's (or region's) primary energy flows, energy distribution system, secondary energy production processes (e.g., electricity generation), and end-use consumption, including a major sub-model of the transport sector which keeps track of the size of vehicle fleets and the penetration rate of alternative fuels. The model enables the comparison of varying strategies for hydrogen introduction against the metrics of overall energy consumption, demands for primary fuel, and carbon dioxide emissions reductions. A case study is presented of the application of THESIS to a high hydrogen penetration scenario within the context of the UK energy economy to 2050, selected from a wider study into potential hydrogen scenarios under different contextual futures [Dutton AG, Bristow AL, Page MW, Kelly CE, Watson J, Tetteh A. The hydrogen economy: its long term role in greenhouse gas reduction. Tyndall Centre Final Report, Project No. IT1.26; November 2004, available from: (http://www.tyndall.ac.uk/research/theme2/final_reports/it1_26.pdf) [last accessed 63 November 2006]. (C) 2006 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.