The mononuclear complex Pd(1‐TosC‐N3)2Cl2 (2) containing 1‐(p‐toluenesulfonyl)cytosine (1) as a ligand, as well as dinuclear complexes Pd2(1‐TosC−‐N3,N4)4 (3) and Pd2(1‐TosC−‐N3,N4)2DMSO2Cl2 (4) containing the ligand anion (1‐TosC−), was mass analyzed by electrospray ionization ion trap MS/MS and high resolution MS. Complexes 3 and 4 were obtained by recrystallization of 2 from DMF and DMSO, respectively. The behavior of complex 2 in different solutions was monitored by electrospray ionization mass spectrometry (ESI‐MS). Under the applied ESI‐MS conditions, complex 2 in methanol reorganized itself dominantly as new complex 3 and the solvent did not coordinate the formed species. In H2O/DMSO, CH3CN/DMSO and CH3OH/DMSO solutions, complex 2 formed several new species with solvent molecules involved in their structure, e.g. complex 4 was formed as the major product. The newly formed species were also examined by LC‐MS‐DAD, confirming the solvent induced reorganization and the solution instability of complex 2. Copyright © 2009 John Wiley & Sons, Ltd.