Recent insights in the field of functional gastrointestinal disorders have opened the way for novel pharmacological treatments directed at the central nervous system or peripheral targets. Now, universally accepted guidelines on therapeutic trial design and in the conduct and reporting of results of large clinical trials in these functional disorders are required. Several lessons have been learned from recent clinical and pharmacological trials of novel agents in irritable bowel syndrome and diabetic dyspepsia. Approaches that carefully characterize the pharmacokinetics, mechanism of action and pharmacodynamics of a drug, and that select subgroups of patients after a thorough understanding of the drug's effects, should facilitate and enhance the likelihood of accurate assessment of potential therapies.