Striatal spine loss is a key pathological feature of Parkinson's disease (PD). Knowing that striatal glutamatergic afferents target dendritic spines, these data appear difficult to reconcile with evidence for an increased expression of the vesicular glutamate transporter 1 (vGluT1) in the striatum of PD patients and 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP)‐treated monkeys, as well as in some electrophysiological studies showing overactivity of the corticostriatal glutamatergic system in models of parkinsonism. To address the possibility that structural changes in glutamatergic afferents may underlie these discrepancies, we undertook an ultrastructural analysis of vGluT1‐positive (i.e., corticostriatal) and vGluT2‐positive (i.e., mostly thalamostriatal) axo‐spinous glutamatergic synapses using a 3D electron microscopic approach in normal and MPTP‐treated monkeys. Three main conclusions can be drawn: 1) spines contacted by vGluT1‐containing terminals have larger volume and harbor significantly larger postsynaptic densities (PSDs) than those contacted by vGluT2‐immunoreactive boutons; 2) a subset of vGluT2‐, but not vGluT1‐immunoreactive, terminals display a pattern of multisynaptic connectivity in normal and MPTP‐treated monkeys; and 3) VGluT1‐ and vGluT2‐positive axo‐spinous synapses undergo ultrastructural changes (larger spine volume, larger PSDs, increased PSD perforations, larger presynaptic terminal) indicative of increased synaptic activity in parkinsonian animals. Furthermore, spines contacted by cortical terminals display an increased volume of their spine apparatus in MPTP‐treated monkeys, suggesting an increased protein synthesis at corticostriatal synapses. These findings demonstrate that corticostriatal and thalamostriatal glutamatergic axo‐spinous synapses display significantly different ultrastructural features, and that both systems undergo complex morphological changes that could underlie the pathophysiology of corticostriatal and thalamostriatal systems in PD. J. Comp. Neurol. 519:989–1005, 2011. © 2010 Wiley‐Liss, Inc.