Evidence for the accumulation and storage of ionized duplex DNA molecules in a quadrupole ion trap is presented. Aqueous solutions of complementary single-strand molecules of DNA were annealed to form duplexes in solution and subjected to electrospray ionization. The ions liberated in this process were transported through an atmosphere/vacuum interface and injected into a quadrupole ion trap operated with a bath gas present at a pressure of 1 mTorr. Despite the roughly 2 order of magnitude poorer signal levels noted for electrospray of aqueous solutions relative to those observed for single-strand oligonucleotides in methanol solutions, aqueous solutions were used to avoid denaturing the duplexes. Ion trap mass spectra are reported here for duplexes consisting of two complementary 20-mer single strands and two complementary 10-mers. Tandem mass spectrometry results are also reported for the 10-mer duplex. These results are significant in that they indicate that the ions are kinetically stable under the ion injection, storage, and mass analysis conditions of the quadrupole ion trap operated with a relatively high pressure of bath gas. The tools of ion trap mass spectrometry can therefore be applied to this important class of compounds.