Ni5Zn21 alloy nanowires were fabricated through template-assisted electrochemical deposition method. The morphology and microstructures of as-deposited nanowires were determined by field-emission scanning electron microscope (FE-SEM), X-ray diffraction (XRD), high-resolution transmission electron microscope (HRTEM), electron diffraction (ED), and electron probe microanalysis (EPMA). The accurate composition was measured via induced coupling plasma atomic emission spectroscopy. SEM results show that Ni5Zn21 nanowires are deposited in most of the nanopores of the template, and they are continuous and dense throughout the whole length. The XRD result demonstrates that the nanowires are mainly composed of a cubic gamma phase Ni5Zn21 alloy, but there also exists a trace of Zn-rich A phase. HRTEM and ED reveal that the alloy nanowires are polycrystalline with the crystallite size of several tens of nanometers. EPMA of a single nanowire illustrates that there exist Ni-rich microzones in as-deposited nanowires. Subsequent magnetic measurements of the array also confirmed the existence of them. In addition, it can be further inferred that the shape of Ni-rich microzones is probably barlike or disklike, from the anisotropy of zero field cooling/field cooling (ZFC/FC) curves as well as the vortex magnetization behavior of the Ni5Zn21 nanowire array. The low-temperature magnetoresistance of the Ni5Zn21 nanowire array was also measured. Giant magnetoresistance instead of anisotropic magnetoresistance is suggested to be responsible for contributing to the magnetoresistance.