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Neurotransmitters are used by the nervous system to transmit messages between neurons. The abnormal levels of the neurotransmitters may lead to neurological disorders. It is very important to monitor their levels in patients. Herein, we report a polymer nanostructured electrode-enabled electrochemical sensing microchip for detecting dopamine and serotonin. The nanostructures on the electrode can enhance the surface area of the electrode dramatically. As a result, the measured electrical signals increased in comparison with those of an electrochemical sensor with an electrode of a flat surface. It has been found that this microchip can detect neurotransmitters with a level as low as ~120 nM with high specificity and can be used to monitor the dopamine and serotonin in a mixed sample successfully in both static and dynamic conditions. Finally, the real-time measurements of dopamine released from N27-A dopaminergic neural cells using the microchip have been demonstrated.