Three flavin-containing compounds, namely, riboflavin, riboflavin 5ῐ-phosphate (flavin mononucleotide, FMN) and flavin-adenine dinucleotide (FAD, Scheme 1), were studied using matrix-assisted laser desorption ionization (MALDI), fast atom bombardment (FAB) and electrospray ionization (ESI) mass spectrometry. It was found that the isoalloxazine ring (flavin) was reduced in the positive-ion MALDI and FAB ionization processes producing unusual ions [Mῌ2] ῌῌ and [Mῌ3] ῌ in addition to the anticipated [Mῌ1] ῌ , whereas ESI generated only [MῌH] ῌ as the molecular-related ion. The reduction mechanism is hypothesized as the protonation from the matrix with a concomitant electron transfer,῏ 1 rather than the transfer of hydrogen atom(s), H ῌ . ESI, in which matrix is not used, did not produce [Mῌ2] ῌῌ nor [Mῌ3] ῌ more than the natural isotope abundance of 13 C in the sample molecules. The reduction site expands to N(1)῎C(10a)῎C(4a)῎N(5), a1,4-diaza-1,3-butadiene system, in the isoalloxazine ring, resembling the behavior of prosthetic groups of aerobic dehydrogenases.