Abstract Graphene is a single-layered sp 2 -hybridized carbon allotrope, which is impermeable to all atomic entities other than hydrogen 1,2 . The introduction of defects allows selective gas permeation 3–5 ; efforts have been made to control the size of these defects for higher selectivity 6–9 . Permeation of entities other than gases, such as ions 10,11 , is of fundamental scientific interest because of its potential application in desalination, detection and purification 12–16 . However, a precise experimental observation of halide permeation has so far remained unknown 11,15–18 . Here we show halide permeation through a single benzene-sized defect in a molecular nanographene. Using supramolecular principles of self-aggregation, we created a stable bilayer of the nanographene 19–23 . As the cavity in the bilayer nanographene could be accessed only by two angstrom-sized windows, any halide that gets trapped inside the cavity has to permeate through the single benzene hole. Our experiments reveal the permeability of fluoride, chloride and bromide through a single benzene hole, whereas iodide is impermeable. Evidence for high permeation of chloride across single-layer nanographene and selective halide binding in a bilayer nanographene provides promise for the use of single benzene defects in graphene for artificial halide receptors 24,25 , as filtration membranes 26 and further to create multilayer artificial chloride channels.