The hypothalamus plays a critical role in maintaining visceral homeostasis. We evaluated, using functional imaging, hypothalamus functional connectivity in adolescent IBS patients and controls who received rectal distension stimulations. More extensive hypothalamus connectivity was observed in liminal than subliminal condition in controls, but not in IBS patients. Compared with controls, IBS patients showed significantly reduced hypothalamus connectivity in the bilateral prefrontal cortices, supplementary motor and premotor areas, bilateral sensorimotor cortex, and limbic subareas, which are specifically involved in homeostatic regulation. The findings support that reduced cortical and limbic modulations of hypothalamus functioning underlies disrupted visceral homeostasis in IBS patients.