Heterostructures of vertically aligned carbon nanotubes (CNTs) and nanostructured silicon were synthesized on quartz substrates using a simple 2 step liquid injection chemical vapor deposition (CVD) approach. The CVD conditions and the process parameters were modified to engineer droplets and thin film morphologies of silicon on the CNTs. The combined influence of these Si morphologies on the electrochemical performance was then studied. Structural analyses conducted on the heterostructures using XRD and Raman spectroscopy indicated the existence of nanocrystalline and amorphous phases of silicon. Cycling performance of these heterostructures exhibit very high specific discharge capacities in excess of 2300mAh/g accompanied by a low irreversible loss (10%) for a loading density of ∼2–3mg/cm2 demonstrating the use of these heterostructures as next generation lithium-ion anodes.