A new portable instrument that includes a high voltage power supply, a bipotentiostat, and a chip holder has been especially developed for using microchips electrophoresis with electrochemical detection. The main unit of the instrument has dimensions of 150 x 165 x 70 mm (w x d x h) and consists of a four-outputs high voltage power supply with a maximum voltage of +/- 3 KV and an acquisition system with two channels for dual amperometric (DC or pulsed amperometric detection) detection. Electrochemical detection has been selected as signal transduction method because it is relatively easily implemented, since nonoptical elements are required. The system uses a lithium-ion polymer battery and it is controlled from a desktop or laptop PC with a graphical user interface based on LabVIEW connected by serial RS232 or Bluetooth (R). The last part of the system consists of a reusable chip holder for housing the microchips, which contain all the electrical connections and reservoirs for making the work with microchips easy. The performance of the new instrument has been evaluated and compared with other commercially available apparatus using single- and dual-channel pyrex microchips for the separation of the neurotransmitters dopamine, epinephrine, and 3,4-dihydroxy-L-phenyl-alanine. The reduction of the size of the instrument has not affected the good performance of the separation and detection using microchips electrophoresis with electrochemical detection. Moreover, the new portable instrument paves the way for in situ analysis making the use of microchips electrophoresis easier.