After entering target regions, afferent growth cones grow among putative target cells, stop extending upon meeting target cells, and transit into a synaptic ending. During these events, signals are transmitted to and from target cells to stimulate programs of differentiation. Here we describe three approaches to unraveling mechanisms of these phases of synaptogenesis. First, dye-labeling in the intact cerebellum has revealed the orchestration of afferent ingrowth and contacts with target cells. Second, an in vitro model based on purified granule neurons has shed light on the role of target cells in the arrest of afferent extension. Third, coculture of purified granule neurons (parallel fiber afferents) with purified Purkinje cells has demonstrated facets of afferent regulation of target cell differentiation. These analyses have suggested molecular mechanisms that mediate maturation of afferents and their targets.