Obstructive sleep apnea syndrome (OSAS) leads to neurocognitive and autonomic deficits that are partially mediated by thalamic and putamen pathology. We examined the underlying neurochemistry of those structures using compressed sensing-based 4D echo-planar J-resolved spectroscopic imaging (JRESI), and quantified values with prior knowledge fitting. Bilaterally increased thalamic mI/Cr, putamen Glx/Cr, and Glu/Cr, and bilaterally decreased thalamic and putamen tCho/Cr and GABA/Cr occurred in OSAS vs healthy subjects (p < 0.05). Increased right thalamic Glx/Cr, Glu/Cr, Gln/Cr, Asc/Cr, and decreased GPC/Cr and decreased left thalamic tNAA/Cr, NAA/Cr were detected. The right putamen showed increased mI/Cr and decreased tCho/Cr, and the left, decreased PE/Cr ratio. ROC curve analyses demonstrated 60-100% sensitivity and specificity for the metabolite ratios in differentiating OSAS vs. controls. Positive correlations were found between: left thalamus mI/Cr and baseline oxygen saturation (SaO 2 ); right putamen tCho/Cr and apnea hypopnea index; right putamen GABA/Cr and baseline SaO 2 ; left putamen PE/Cr and baseline SaO 2 ; and left putamen NAA/Cr and SaO 2 nadir (all p < 0.05). Negative correlations were found between left putamen PE/Cr and SaO 2 nadir. These findings suggest underlying inflammation or glial activation, with greater alterations accompanying lower oxygen saturation. These metabolite levels may provide biomarkers for future neurochemical interventions by pharmacologic or other means.Obstructive sleep apnea syndrome (OSAS) is a common sleep disorder, characterized by repeated intermittent hypoxic episodes 1 from obstructed breathing. The repeated apneas result in multiple cognitive, mood, autonomic, neuroendocrine, and excessive sleepiness deficits, presumably from neural injury in brain structures serving those functions 2-7 . Although multiple brain sites mediate these symptoms, two structures, the thalamus which serves essential sensory processing, cortical activation, and autonomic roles, and the putamen which serves significant autonomic and motor regulatory needs, are of particular importance. Both structures show volumetric and water diffusion changes in OSAS 8,9 , but processes underlying the nature of the OSAS injury found in those structures are unclear.The putamen serves essential roles in autonomic regulation, a major concern in OSAS given the poor sympathetic control in the condition. Damage to the putamen is associated with pathological conditions including Multiple Systems Atrophy 10 . The putamen heavily participates in cognitive behavior, including executive function and working memory, with extensive projections via frontostriatal circuit to the frontal cortex 11 . Injury to the putamen will also affect somatic motor control, which poses concerns for upper airway muscle dysfunction 8,12 underlying airway collapse in OSAS.The thalamus was selected for evaluation because of its major role in bidirectional transmission of neural signals between cortical and subcortical regions, an inter...