The development of dendrites is a crucial step in the formation of cortical circuitry. The morphogen brain-derived neurotrophic factor (BDNF) may mediate the effects of activity on dendritic morphology since its expression and release are thought to be activity-dependent. Using two-photon microscopy, the autocrine and paracrine effects of BDNF on dendritic morphology were assessed. Overexpression of BDNF profoundly altered the form and stability of basal dendritic arbors via an autocrine mechanism. Paracrine BDNF also altered dendritic branching, though in a highly local fashion. BDNF is capable of acting as an intercellular morphogen, and could hypothetically shape dendritic arbors to best fit the developing structure and function of the pre-synaptic circuit.