The complex dendrimeric contrast agent Gadomer has been comprehensively characterized using various mass spectrometric techniques in combination with capillary electrophoresis. The analytical challenges arising from the structure of this analyte, e.g., the presence of a complex isotopic pattern originating from multiple gadolinium chelates could be overcome using this combined approach. Results obtained from initial MALDI-TOF-MS measurements could subsequently be complemented and confirmed by CE-ESI-TOF-MS measurements. Furthermore, high resolution Fourier transform-ion cyclotron resonance-MS (FT-ICR-MS) as a stand alone technique and in combination with CE was performed to obtain mass spectra of high mass accuracy and resolution of various impurities and related dendrimers present in low concentrations in several Gadomer batches. The profile of related dendrimers and impurities of lower molecular weight present in Gadomer could be elucidated and variances in the pattern of related dendrimers present in batches obtained via different synthetic routes could be detected. The qualitative analysis of Gadomer using MS techniques in combination with CE provides the fundamental basis for a framework of analytical methodologies for the characterization of Gadomer. By designing such a framework of methodologies the challenges associated with the introduction of dendrimers into the clinical stage may be overcome and the reproducible quality and safety of these innovative products can be ensured.