Transition metal ions and radicals in flours of various botanical origins with different content of starch have been studied by EPR before and after thermal treatment. The amounts of metal ions, have been determined by ICP OES. Simulations of EPR spectra have revealed the presence of several types of radicals (carbon-centred, tyrosyl and semiquinone) localized in starch and protein fractions of flours. Thermal treatment of flours significantly increased the amount of radicals with a simultaneous decrease of the signal intensity of transition metal ions. The proposed mechanism of thermal generation of stable organic radicals was associated with the redox processes involving transition metal ions, which facilitated the formation of radicals. The dependence between the way starch is treated and the mechanism of radical formation was also shown.