The habenula is a hub for cognitive and emotional signals that are relayed to the aminergic centers in the midbrain and, thus, plays an important role in goal-oriented behaviors. Although it is well described in rodents and non-human primates, the habenula functional network remains relatively uncharacterized in humans, partly because of the methodological challenges associated with the functional magnetic resonance imaging of small structures in the brain. Using high-resolution cardiac-gated resting state imaging in healthy humans and precisely identifying each participants' habenula, we show that the habenula is functionally coupled with the insula, parahippocampus, thalamus, periaqueductal grey, pons, striatum and substantia nigra/ventral tegmental area complex. Furthermore, by separately examining and comparing the functional maps from the left and right habenula, we provide the first evidence of an asymmetry in the functional connectivity of the habenula in humans. Hum Brain Mapp 37:2602–2615, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.