Complexes of copper (II) ions and uracil were studied using tandem mass spectrometry (Fourier transform ion cyclotron resonance, FTICR, mass spectrometry) including extensive isotopic labeling as well as theoretical calculations. Positive ion electrospray mass spectra of aqueous solutions of CuCl2 and uracil show that the [Cu(Ura-H)(Ura)]+ ion is the most abundant ion even at low concentrations of uracil. Sustained off-resonance irradiation collision-induced dissociation (SORI-CID) experiments show that the lowest energy decomposition pathway for [Cu(Ura-H)(Ura)]+, surprisingly, is not the loss of uracil, but the loss of HNCO followed by HCN as the most abundant secondary fragmentation product. MSn studies identified primary, secondary and tertiary fragmentation products. Extensive isotopic labeling studies, as well as computational studies allowed for a detailed fragmentation scheme for the [Cu(Ura-H)(Ura)]+ ion, beginning with the lowest energy structure.