We report the formation of single crystal MnSi nanowires, MnSi/Si/MnSi nanowire heterostructures, to study the spin transport in silicon nanostructure. Scanning electron microscopy studies show that silicon nanowires can be converted into single crystal MnSi nanowires through controlled solid-state reaction. High-resolution transmission electron microscope studies show that MnSi/Si/MnSi heterostructures have clean, atomically sharp interfaces with an epitaxial relationship of Si//MnSi and Si(345)//MnSi(214). Magnetoresistance (MR) studies show that the single crystal MnSi nanowire exhibits metallic behavior with paramagnetic to ferromagnetic transition temperature of 29.7 K and a negative MR up to 1.8% at low temperature. Furthermore, using single crystal MnSi/p-Si/MnSi nanowire heterostructures, we have studied carrier tunneling via the Schottky barrier and spin polarized carrier transport in the silicon nanodevices.