Highly reliable and accurate analytical methods are needed for the determination of magnetic resonance imaging (MRI) contrast agents in complex matrices of clinical interest. We demonstrate the reliability of capillary zone electrophoresis (CZE) coupled with electrospray ionization-mass spectrometry (ESI-MS) for the analysis of MultiHance (gadobenate dimeglumine), a gadolinium-based MRI agent. A sheath liquid interface connected the CE system with an electrospray mass spectrometer equipped with an ion-trap analyzer. CZE with ultraviolet (CZE-UV) and with mass detection (CZE-MS) were compared by analyzing gadobenate dimeglumine and the free ligand diluted in water and in biological fluids (i.e., human serum and urine). The optimization of some relevant CZE-MS parameters was accomplished, like CE buffer composition, sheath liquid composition and flow, and type and length of the separation capillary. CZE-UV was highly influenced by the biological sample components, which hindered a reliable quantification of both gadobenate and free ligand in serum and urine. In CZE-MS, on the other hand, the electrophoretic runs turned out to be independent of the clinical matrices, due to the informative potential and to the selectivity of MS detection.