Proper brain function is tightly controlled by neurochemically active compounds (NACs). These NACs can be directly detected in the brain. However the actual NACs and their metabolites can also be monitored in the blood. Measuring the concentrations and ratios of NACs simultaneously collected in the blood and brain can therefore provide important insights in their intracortical release and metabolism. This will allow interpolation of brain NACs concentrations/ratios from systemically sampled NACs concentrations (blood), which can serve as biomarker for dysfunctional processes in the brain. We report here a method for the simultaneous neurochemical analysis of five polar compounds, acetylcholine, lactate, pyruvate, glutamine and glutamate. We sampled these NACs from venous blood as well as intracortically from the primary visual cortex of anesthetized non-human primates during visual stimulation. Simultaneous systemic and intracortical microdialysis was used for sample collection. Great care was taken to synchronize to two sampling devices and to adjust the sample preparation for direct comparability. After sample collection we used a capillary hydrophilic interaction liquid chromatography (HILIC) for optimal separation of the sample’s components. For detection of the NACs tandem mass spectrometry (MS/MS) was coupled to HILIC without using an