As a first step towards a consistent framework for both individual and comparative life cycle assessment (LCA) of hydrogen energy systems, this work performs a thorough literature review on the methodological choices made in LCA studies of these energy systems. Choices affecting the LCA stages "goal and scope definition", "life cycle inventory analysis" (LCI) and "life cycle impact assessment" (LCIA) are targeted. This review considers 97 scientific papers published until December 2015, in which 509 original case studies of hydrogen energy systems are found. Based on the hydrogen production process, these case studies are classified into three technological categories: thermochemical, electrochemical and biological. A subdivision based on the scope of the studies is also applied, thus distinguishing case studies addressing hydrogen production only, hydrogen production and use in mobility and hydrogen production and use for power generation. Most of the hydrogen energy systems apply cradle/gate-to-gate boundaries, while cradle/gate-to-grave boundaries are found mainly for hydrogen use in mobility. The functional unit is usually mass- or energy-based for cradle/gate-to-gate studies and travelled distance for cradle/gate-to-grave studies. Multifunctionality is addressed mainly through system expansion and, to a lesser extent, physical allocation. Regarding LCI, scientific literature and life cycle databases are the main data sources for both background and foreground processes. Regarding LCIA, the most common impact categories evaluated are global warming and energy consumption through the IPCC and VDI methods, respectively. The remaining indicators are often evaluated using the CML family methods. The level of agreement of these trends with the available FC-HyGuide guidelines for LCA of hydrogen energy systems depends on the specific methodological aspect considered. This review on LCA of hydrogen energy systems succeeded in finding relevant trends in methodological choices, especially regarding the frequent use of system expansion and secondary data under production-oriented attributional approaches. These trends are expected to facilitate methodological decision making in future LCA studies of hydrogen energy systems. Furthermore, this review may provide a basis for the definition of a methodological framework to harmonise the LCA results of hydrogen available so far in the literature.