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Doped semiconductor nanowires are emerging as next-generation electronic colloidal materials, and the efficient manipulation of such nanostructures is crucial for technological applications. In fluid suspension, pn nanowires (pn NWs), unlike homogeneous nanowires, have a permanent dipole, and thus, experience a torque under an external DC field that orients the nanowire with its n-type end in the direction of the field. Here, we quantitatively measure the permanent dipoles of various Si nanowire pn diodes and investigate their origin. By comparing the dipoles of pn NWs of different lengths and radii, we show that the permanent dipole originates from non-uniform surface-charge distributions, rather than the internal charges at the p–n junction as was previously proposed. This understanding of the mechanism for pn NWs orientation has relevance to the manipulation, assembly, characterization, and separation of nanowire electronics by electric fields.