The growing evidence for a key role of psychophysiological processes in the etiopathogenesis of functional gastrointestinal disorders (FGID) originates from various sources, including epidemiological, psychometric, physiological, and behavioural studies. Functional neuroimaging has improved our knowledge about central processing of visceral pain, a defining feature of FGID. However, results have been disappointingly inconsistent, often due to psychosocial factors not being controlled for. In this paper, we aim to show that using integrated research strategies, encompassing a number of scientific disciplines, is critical to advancing our understanding of FGID. We will illustrate this by describing recent integrative studies that may serve as good examples. More specifically, future FGID neuroimaging studies should control for psychosocial factors and incorporate methods from other branches of neuroscience outside this field, especially cognitive, affective and autonomic neuroscience. We therefore propose a framework for the development of an integrative cross-disciplinary research strategy based on advancing our understanding of visceral nociceptive physiology in health as well as vulnerability and susceptibility factors for FGID. This approach will allow the identification of factors responsible for the inter-individual differences in visceral pain perception and susceptibility to chronic visceral pain, leading to the description of multidimensional (visceral) pain "endophenotypes." These may represent the critical steps needed towards a pathophysiological, rather than symptom-based, classification of FGID, which may be more suitable for genetic association studies. This approach may ultimately culminate in individual tailoring of treatment, in addition to disease prevention, thereby improving outcomes for the patient and researcher alike.