Objective To investigate the effects of intranigral injection of glutamate and gama amino butyric acid (GABA) on iron metabolism in the caudate putamen nucleus of rats. Methods Glutamate and GABA respectively were stereotaxically injected into the substantia nigra of rats. The levels of iron in the caudate putamen nucleus were detected by spectrophotometer. The levels of tyrosine hydroxylase (TH) in the substantia nigra, divalent metal transporter 1 without iron response element in the 3′-UTR (DMT1-IRE) and hephaestin (HP) in the caudate putamen nucleus were also detected by immunohistological study. Results The levels of iron in the caudate putamen nucleus of the mono sodium glutamate (MSG) group increased dramatically, while the levels of iron in GABA group decreased with no obvious change. Both the expression of TH in the MSG group and GABA group showed no differences when compared to controls. The levels of DMT1-IRE in the caudate putamen nucleus of the MSG group increased dramatically, while the levels of DMT1-IRE in the GABA group decreased dramatically. However, the levels of HP in the caudate putamen nucleus of MSG group decreased dramatically, while the levels of HP in GABA group increased dramatically. Conclusion Glutamate and GABA in the substantia nigra may affect iron metabolism through DMT1-IRE and HP in the caudate putamen nucleus.