Hydrogen (H2)-rich fluids are observed in a wide variety of geologic settings including gas seeps in serpentinized ultramafic rocks, sub-seafloor hydrothermal vents, fracture networks in crystalline rocks from continental and oceanic crust, and volcanic gases. Natural hydrogen sources can sustain deep microbial ecosystems, induce abiotic hydrocarbons synthesis and trigger the formation of prebiotic organic compounds. However, due to its extreme mobility and small size, hydrogen is not easily trapped in the crust. If not rapidly consumed by redox reactions mediated by bacteria or suitable mineral catalysts it diffuses through the rocks and migrates toward the surface. Therefore, H2is not supposed to accumulate in the crust. We challenge this view by demonstrating that significant amount of H2may be adsorbed by clay minerals and remain trapped beneath the surface. Here, we report for the first time H2content in clay-rich rocks, mainly composed of illite, chlorite, and kaolinite from the Cigar Lake uranium ore deposit (northern Saskatchewan, Canada). Thermal desorption measurements reveal that H2is enriched up to 500 ppm (i.e. 0.25molkg−1of rock) in these water-saturated rocks having a very low total organic content (<0.5 wt%). Such hydrogen uptake is comparable and even exceeds adsorbed methane capacities reported elsewhere for pure clay minerals or shales. Sudoite (Al–Mg di-trioctahedral chlorite) is probably the main mineral responsible for H2adsorption in the present case. The presence of multiple binding sites in interlinked nanopores between crystal layers of illite-chlorite particles offers the ideal conditions for hydrogen sorption. We demonstrate that 4 to 17% of H2produced by water radiolysis over the 1.4-Ga-lifetime of the Cigar Lake uranium ore deposit has been trapped in the surrounding clay alteration haloes. As a result, sorption processes on layered silicates must not be overlooked as they may exert an important control on the fate and mobility of H2in the crust. Furthermore, the high capacity of clay minerals to sorb molecular hydrogen may also open up new opportunities for exploration of unexpected energy resources and for H2storage based on geo-inspired materials.