Over the past few years, there have been dramatic changes in our understanding of the role of endogenous 5-hydroxytryptamine (5-HT) in the generation of gastrointestinal (GI) motility patterns in the small and large intestine. The idea that endogenous 5-HT played a major role in the generation of peristalsis in the small intestine was first proposed in the mid 1950s, after it was discovered that endogenous 5-HT could be released from the mucosa at a similar time that peristalsis occurred; and that exogenous 5-HT could potently stimulate peristalsis. The fact that exogenous 5-HT stimulated peristalsis and that there was a similarity in timing between the release of 5-HT from the mucosa and the onset of peristalsis led investigators to propose that release of endogenous 5-HT from the mucosa was causally related to the generation of peristalsis. In further support of this, other studies showed that selective 5-HT antagonists could inhibit or block peristalsis, and other motor patterns, such as the migrating motor complex. Taken together, based on these findings, some laboratories believed that endogenous 5-HT (synthesized in the gut wall) was an important mediator, or initiator, of different propulsive motor patterns in the lower GI tract. This notion changed dramatically in the past few years, however, after it was discovered that removal of the mucosa abolished all cyclical release of endogenous 5-HT, but did not block peristalsis, nor the cyclical migrating complex. Furthermore, other laboratories revealed that genetic deletion of the gene tryptophan hydroxylase 1 (TPH-1) (that synthesizes endogenous 5-HT in the mucosa) actually had no inhibitory effect on transit of intestinal contents in live animals. Then, perhaps one of the most startling of all observations was the discovery that selective 5-HT receptor antagonists actually have the same inhibitory effects on peristalsis and the migrating complex in segments of intestine that had been depleted of all endogenous 5-HT. Taken together, these recent findings have led to a major revision in our understanding of the functional role of endogenous 5-HT in the generation of propulsive motor patterns in the lower GI tract. This review will focus on how our understanding of endogenous 5-HT in the GI tract has changed substantially in recent times.