G-quadruplexes are four-stranded nucleic acid structures typically made up of stacked GGGG tetrads connected by short loops [1]. Although most studies investigating potential biological roles of G-quadruplexes have focused on monomeric structures, recent work suggests that multimeric G-quadruplexes could also be important. We recently identified mutations in the central tetrad of a monomeric G-quadruplex that induce formation of higher-order structures [2-4]. Here we show that both DNA-DNA and DNA-RNA G-quadruplexes containing a guanosine to adenosine mutation at a specific position in this tetrad behave like molecular switches in which the equilibrium between monomeric and multimeric G-quadruplex is controlled by GTP concentration. Analysis of the nucleotide specificity of inhibition and characterization of the mechanism of binding by NMR suggest that GTP stabilizes the monomeric form of the G-quadruplex by becoming incorporated into one of the tetrads. Hundreds of sequences with the potential to form such GTP-dependent switches are present in the human genome, including some that are evolutionarily conserved. Our experiments provide new insights into the small molecule-mediated control of G-quadruplex multimerization, and raise the possibility that a GTP-dependent switch controls G-quadruplex multimer formation in cells.