Ab initio molecular orbital theory was used to investigate the structure of flavin in different oxidation and protonation states using lumiflavin as a model compound. According to our study, oxidized flavin is planar no matter what its protonation state or whether it participates in hydrogen bonding. The structures of flavin semiquinone radicals are planar or very close to planar, but the reduced flavin H(3)Fl(red) (9) is bent with a ring puckering angle of 27.3 degrees along the N5 and N10 axis. The calculations indicate that N1 is the site of protonation for oxidized flavin, which is in agreement with several crystallographic studies. The calculated spin density distribution for flavin semiquinone radicals is also consistent with experimental results. Electrostatic potential derived charges at the RHF/6-31G* level of theory are also provided for both oxidized and reduced flavins.