One of the strategies to improve cochlear implant technology is to increase the number of electrodes in the neuro-electronic interface. The objective was to characterize in vitro cultures of spiral ganglion neurons (SGN) cultured on surfaces of novel silicon micro-pillar substrates (MPS). SGN from P5 rat pups were cultured on MPS with different micro-pillar widths (1–5.6 μm) and spacings (0.6–15 μm) and were compared with control SGN cultures on glass coverslips by immunocytochemistry and scanning electron microscopy (SEM). Overall, MPS support SGN growth equally well as the control glass surfaces. Micro-pillars of a particular size-range (1.2–2.4 μm) were optimal in promoting SGN presence, neurite growth and alignment. On this specific micro-pillar size, more SGN were present, and neurites were longer and more aligned. SEM pictures highlight how cells on micro-pillars with smaller spacings grow directly on top of pillars, while at wider spacings (from 3.2 to 15 μm) they grow on the bottom of the surface, losing contact guidance. Further, we found that MPS encourage more monopolar and bipolar SGN morphologies compared to the control condition. Finally, MPS induce longest neurite growth with minimal interaction of S100+ glial cells. These results indicate that silicon micro-pillar substrates create a permissive environment for the growth of primary auditory neurons promoting neurite sprouting and are a promising technology for future high-density three-dimensional CMOS-based auditory neuro-electronic interfaces.