Although nanowires are widely used in biological applications, especially as cell-manipulation tools, the effect of nanowires on living cells has not been fully investigated. Here, we examined the full gene expression of mouse cortical stem cells cultured on vertical nanowire substrates using RNA microarrays. Genes involved in cell adhesion, cell morphology regulation and cell metabolism were up regulated on the nanowire substrates as compared to flat controls. Scanning electron microscopy images of the samples corroborated our findings, revealing significant differences in cell morphology and adhesion between the nanowire and the flat substrates. Cells on nanowires exhibited a round morphology with a mature appearance characterized by numerous and long processes adhering to the nanowires, while cells on flat substrates had a flat, spread-out morphology and very little neurite outgrowth.