Biogenic amines derived from basic and aromatic amino acids (B/A-BAs), polyamines, histamine, serotonin, and catecholamines are a group of molecules playing essential roles in many relevant physiological processes, including cell proliferation, immune response, nutrition and reproduction. All these physiological effects involve a variety of tissue-specific cellular receptors and signalling pathways, which conforms to a very complex network that is not yet well-characterized. Strong evidence has proved the importance of this group of molecules in the gastrointestinal context, also playing roles in several pathologies. This work is based on the hypothesis that integration of biomedical information helps to reach new translational actions. Thus, the major aim of this work is to combine scientific knowledge on biomolecules, metabolism and physiology of the main B/A-BAs involved in the pathophysiology of the gastrointestinal tract, in order to point out important gaps in information and other facts deserving further research efforts in order to connect molecular information with pathophysiological observations.