Extensive experimental investigations along with high speed visualizations have been performed to assess the flow boiling characteristics in Silicon Nanowire (SiNW) microchannels. Experiments have been also performed in Plainwall microchannels to compare their performances with SiNW configurations. HFE-7100 has been used as the working fluid and experiments are conducted in a forced convection loop at mass flux range of 400–1600 kg/m2s. Arrays of microchannel consist 5 (five) parallel straight microchannels with Width, Depth and Length dimension of 220 μm, 250 μm and 10 mm respectively. Flow boiling performances including heat transfer coefficient (HTC), pressure drop, two-phase flow instabilities and critical heat flux (CHF) have been studied in both the Silicon plainwall (smooth inner surface) and Silicon Nanowire (silicon nanostructured inner surface) microchannels. High speed flow visualizations have been performed at up to 70,000 frames per s (fps) to understand the difference in boiling mechanisms between Plainwall and SiNW. SiNW performs significantly enhanced HTC (up to 400% improvement), reduces flow boiling instabilities and pressure drop (up to 70% reduction) compared to Plainwall microchannels. However, little/insignificant effect of nanostructured surface has been observed on CHF. In addition, a major difference in two-phase flow regime development has been observed between the SiNW and Plainwall microchannels during flow visualization. Specifically, SiNWs introduce explosive bubble nucleation, reduce intermittent flow regimes (slug/churn), improve rewetting, maintain thin liquid film and thus, improve system performances.