Holes with an average size of 2-5 nm have been created in graphene layers by heating of graphite oxide (GO) in concentrated sulfuric acid followed by annealing in an argon flow. The hot mineral acid acts simultaneously as a defunctionalizing and etching agent, removing a part of oxygen-containing groups and lattice carbon atoms from the layers. Annealing of the holey reduced GO at 800 °C-1000 °C causes a decrease of the content of residual oxygen and the interlayer spacing thus producing thin compact stacks from holey graphene layers. Electrochemical tests of the obtained materials in half-cells showed that the removal of oxygen and creation of basal holes lowers the capacity loss in the first cycle and facilitates intercalation-deintercalation of lithium ions. This was attributed to minimization of electrolyte decomposition reactions, easier desolvation of lithium ions near the hole boundaries and appearance of multiple entrances for the naked ions into graphene stacks.