The present study establishes a method for the separation and characterization of rabbit liver metallothionein (MT) subisoforms by capillary electrophoresis coupled to electrospray ionization time-of-flight mass spectrometry (CE-ESI-TOF-MS) via a sheath-flow interface. Directly coupled-CE-MS enables the extraction of specific molecular weight information and thereby facilitates the identification of peaks when no reference materials are available, as in the case of MT subisoforms. The analysis described here revealed the presence of the apothioneins MT-1a, MT-2d, and MT-2e, belonging to MT-I sample, and MT-2a, MT-2b, and MT-2c, belonging to MT-II. Several non-N-acetylated forms were also detected as traces appearing with their respective acetylated forms in both samples. Similar results were found when MALDI-TOF experiments were performed, identifying all the sequenced rabbit liver MTs as apo-MT-forms, as in the CE-ESI-MS coupling.