Silicon is one of the most attractive anode materials for use in Li-ion batteries due to its ∼10 times higher specific capacity than existing graphite anodes. However, up to 400% volume expansion during reaction with Li causes particle pulverization and fracture, which results in rapid capacity fading. Although Si nanomaterials have shown improvements in electrochemical performance, there is limited understanding of how volume expansion takes place. Here, we study the shape and volume changes of crystalline Si nanopillars with different orientations upon first lithiation and discover anomalous behavior. Upon lithiation, the initially circular cross sections of nanopillars with <100>, <110>, and <111> axial orientations expand into cross, ellipse, and hexagonal shapes, respectively. We explain this by identifying a high-speed lithium ion diffusion channel along the <110> direction, which causes preferential volume expansion along this direction. Surprisingly, the <111> and <100> nanopillars shrink in height after partial lithiation, while <110> nanopillars increase in height. The length contraction is suggested to be due to a collapse of the {111} planes early in the lithiation process. These results give new insight into the Si volume change process and could help in designing better battery anodes.