An end-channel amperometric detector with a guide tube for working electrode was designed and integrated on a home-made glass microchip. The guide tube was directly patterned and fabricated at the end of the detection reservoir, which made the fixation and alignment of working electrode relatively easy. The fabrication was carried out in a two-step etching process. A 30 m carbon fiber microdisk electrode and Pt cathode were also integrated onto the amperometric detector. The characteristics and primary performance of the home-made microchip capillary electrophoresis (MCCE) were investigated with neurotransmitters. The baseline separation of dopamine (DA), catechol (CA) and epinephrine (EP) was achieved within 80 s. Separation parameters such as injection time, buffer components, pH of the buffer were studied. Relative standard deviations of not more than 6.0% were obtained for both peak currents and migration times. Under the selected separation conditions, the response for DA was linear from 5 to 200 M and from 20 to 800 M for CA. The limits of detection of DA and CA were 0.51 and 2.9 M, respectively (S/N = 3).