A mass spectral characterization of a set of anthracyclines and anthracyclinones comprised of daunorubicin, adriamycin and their modified analogs was carried out by using negative and positive fast atom bombardment (FAB) ionization techniques. Addition of more than one hydrogen to the molecular ions of the anthracyclines was observed. The choice of the FAB matrix played an important role in the characterization of these compounds. The dominant ions in the molecular ion region were M-. (or M+.) and MH- (or MH+.2) when sulfolane and glycerol, respectively, were employed as the FAB solvents. The major fragmentation was cleavage of the glycosidic bond with the charge retention mainly on the aglycone moiety. Aromatization of the tetracyclic ring promoted further fragmentation of the aglycone moiety. The anthracyclinones could be characterized only by negative FAB ionization using sulfolane as the FAB matrix. The assigned fragmentation pathways were confirmed by acquiring metastable ion spectra using B/E linked-field scans.