Serotonin (5-HT) and melatonin (MEL) are well known neurotransmitters and paracrine signalling molecules. Both compounds are present in enterochromaffin (EC) cells in the mucosa of the gastrointestinal tract and are thought to play a role in controlling gut motility. To date there are no real-time analytical methods for the detection of these two molecules and it is not clear if MEL is actually released from the EC cells. In this paper, I used boron-doped diamond (BDD) microelectrodes to record 5-HT and MEL overflow from EC cells in the mucosa of rabbit ileum. The BDD microelectrode was extremely stable and sensitive for measurements of both compounds when assessed using differential pulse voltammetry (DPV) and flow injection analysis (FIA) using amperometric detection. MEL release was detected in the mucosa, where it is most likely from the EC cells. Mechanical stimulation of individual villi increased 5-HT but not MEL overflow. Application of the serotonin transporter (SERT) inhibitor, fluoxetine, elevated the 5-HT but not the MEL signal. Differences in the amounts of the two gastrointestinal compounds released and the mechanism of which they are released will provide insights to the physiology of the EC cell and disease states.