The melanocortin 4 receptor (MC4R) plays a prominent role in hypothalamic weight regulation. Activation of this receptor results by so far not understood mechanisms in a decrease of food-intake and an increase of energy expenditure. Recently a functional role downstream of MC4R signalling for brain derived neurotrophic factor (BDNF) and its receptor tropomyosin-related kinase B receptor (TrkB) was reported. TrkB signalling influences several neuronal processes like synapse formation and long-term potentiation Mutations in human TrkB gene NTRK2 cause severe hyperphagia, obesity, developmental delay and deficits in memory and learning.To understand the physiological role of TrkB in hypothalamic weight regulation and to identify further downstream signalling pathways of TrkB we used different fragments of TrkB as baits in a yeast-two-hybrid screen against prays derived from a human brain cDNA library. We found an interaction of the Shc binding site containing juxtamembrane domain of TrkB with the neuron specific Septin Sept3b. This interaction was confirmed by in vitro Gluthathion S-Transferase (GST)-pulldown experiments using GST-tagged Sept3 and the HA-tagged intracellular TrkB domain. Furthermore we could show in vitro that the interaction is independent of the phosphorylation of the Shc.-binding site of TrkB and splice variants of Sept3, but dependent on a short sequence motif that has previously been described to be important for the intracellular trafficking of TrkB. In differentiated PC12 cells we could show intracellular colocalization of both full-length proteins. Our results provide a first hint for a connection between BDNF signalling and Sept3 that has to be further elucidated in a neuronal cell system.