PSD-95, a synaptic scaffolding protein, plays important roles in the regulation of dendritic spine morphology and glutamate receptor signaling. We have recently shown that PSD-95 also plays an extrasynaptic role during development. PSD-95 shapes dendrite branching patterns in cultured rat hippocampal neurons by altering microtubule dynamics via an association with the microtubule end-binding protein-3 (EB3). We discovered that PSD-95 interacts directly with EB3 and that the result of this interaction decreases EB3 binding to and EB3 comet lifetime on microtubules. This decrease in lifetime also correlates to decreased dendrite branching. Here we present an additional effect of PSD-95 overexpression on microtubules. Neurons that overexpress PSD-95 show increased distance between microtubules in a manner that is not fully dependent on the interaction between PSD-95 and EB3. We discuss these new data in the context of the role of PSD-95 in shaping the dendritic arbor, and we extend our findings to include a discussion of how PSD-95 may guide neurons toward a more mature and synapse-oriented growth stage.