The European Organization for Nuclear Research (CERN) is currently undertaking a feasibility study to build the next-generation particle accelerator, named the Future Circular Collider (FCC), hosted in a 90–100 km subsurface infrastructure in the Geneva Basin, extending across western Switzerland and adjacent France. This article represents a preliminary, basin-scale stratigraphic and lithotype analysis using state-of-the-art Swiss and French stratigraphic terminology, set in context with the FCC. Existing stratigraphic information, rock cores and well reports, laboratory analyses and geophysical well-logs from 661 wells representative for the construction area have been integrated to pave the way for a multidisciplinary approach across several geoscientific and engineering domains to guide the FCC’s upcoming technical design phase. Comparisons with well-log data allowed the identification of rock formations and lithotypes, as well as to formulate a preliminary assessment of potential geological hazards. Regional stratigraphic evaluation revealed the FCC’s intersection of 13 geological formations comprising 25 different lithotypes across the Geneva Basin. A lack of data remains for the western to south-western subsurface region of the FCC construction area shown by well-density coverage modelling. The main geological hazards are represented by karstic intervals in the Grand Essert Formation’s Neuchâtel Member, Vallorbe and Vuache formations, associated to fractured limestone lithotypes, and Cenozoic formations represented by the pure to clayey sandstone-bearing Transition zone and Siderolithic Formation. Potential swelling hazard is associated to the presence of anhydrite, and claystone lithotypes of the Molasse Rouge and Grès et Marnes Gris à gypse formations, yielding up to 17.2% of smectite in the Molasse Rouge formation. Hydrocarbon indices in both gaseous and bituminous forms are encountered in the majority of investigated wells, and bear a potential environmental hazard associated with the Molasse Rouge deposits and fractured limestones of the Mesozoic Jura formations.