In the last decade, silicon nanowires (SiNWs) have attracted more attentions due to their excellent electrical and optical properties, and they also promise great applications in diverse fields including Raman silicon laser, antireflective solar cell, and highly sensitive biological sensors. Recently, the application of SiNWs has been extended into the biological field based on their controllable electrical property and superhydrophilic property. In addition to their electrical and surface property, a great amount of studies indicated that nano-topography can enhance cellular viability and physiological functions. Therefore, SiNWs may play a significant role as an in vitro cell culture matrix due to the aforementioned properties. For in vivo cell culture, it should be noticed that a neuron is an electrically excitable cell that transmits information by electrochemical impulses. Unfortunately, the function of the mammalian nervous system still remains unclear. Therefore, some researchers attempt to culture neurons in vitro to operate fundamental studies or to reverse-engineer the nervous system. However, neurons grow and differentiate into randomly connected neuronal populations on commercial culture plates. Researchers can merely measure behaviors of homogeneous neuronal circuits. The response of structured organization and controlled connectivity similar to those found in the nervous system are lacking. Consequently, we propose to figure out the cytotoxicity of mouse fibroblasts (L929) and pheochromocytom neurons (PC12) on various types of SiNWs and flat Si chips, for analyzing their cellular metabolic activity, cell adhesion and growth behaviors. Furthermore we also attempt to culture neurons on SiNWs chips with micropatterns in order to guide neurites growth direction for in vitro neuronal engineering. In this study, we fabricated SiNWs with different lengths employing the EMD method. Our results indicate that SiNWs are well aligned on Si chips and the diameter falls between 103.7-248.2 nm. Such highly rough and well-aligned SiNWs therefore possess superhydrophilic properties that may favor cell adhesion and following growth behavior and differentiation. We found that SiNWs can be regarded as a non-cytotoxic matrix when cultured with L929 and PC12, and further provide a better affinity to enhance cell adhesion compared to flat Si and nitride layer. These phenomena dominantly depend on the superhydrophilic and highly rough surface of SiNWs enabling to enhance high protein adsorption rate during cell adhesion. By combining different cell-adhesion affinities of SiNWs and nitride onto a line-pattern substrate, the majority of neurons culturing on SiNW micropatterns with 5-μm width of line pattern selectively grow and extend along SiNWs patterns instead of nitride region. The selective growth direction supposed to be guided by the rough surface and superhydrophilic property of SiNWs allowing higher protein adsorption than nitride. The ability of SiNW-micropattern chips for guiding neurite successfully demonstrated in this study will be a potential tool for neuronal engineering in the future.