Nine areas of the brain were studied by electron paramagnetic resonance spectroscopy and total reflection X-ray fluorescence spectroscopy to measure paramagnetic metal ions, free radicals (neuromelanin), and total metal content. We also determined the extent of accumulation of metal ions by melanins incubated in homogenates of a region of the brain (putamen). The electron paramagnetic resonance spectra of metal ions varied considerably among areas of the brain. There was no correlation between total content of particular metal ions (iron was especially pertinent) and the observed electron paramagnetic resonance spectra, except that the substantia nigra appeared more consistently to have a prominent g = 4 electron paramagnetic resonance signal characteristic of ferric iron in a rhombic state. Only the substantia nigra, and to a lesser extent the locus coeruleus, had a free radical signal consistent with that of neuromelanin. This signal was much more prominent in the unprocessed substantia nigra but when metal ions were removed (reducing the amount of suppression of the electron paramagnetic resonance signal of neuromelanin due to dipole-dipole broadening from nearby metal ions), the electron paramagnetic resonance spectrum of neuromelanin of the locus coeruleus increased much more than that of the substantia nigra. This suggests that the structure of the pigment may differ in these two regions. Incubating synthetic melanins with homogenates of putamen resulted in accumulation of metal ions on the melanins with the concentrations of the three metal ions, relative to their values in the putamen, increasing by factors of 20-30, 3-4, and 25-30, for iron, copper, and zinc, respectively. This suggests that the metal content of isolated neuromelanin may include metal ions which became bound to the neuromelanin during the isolation procedure.