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In neural prosthetic systems, a low-impedance electrode-tissue interface is important for maintaining signal quality for recording, as well as effective charge transfer for stimulation. However, neural microelectrodes often have high impedance due to their small surface areas. In this paper, we present a simple method of increasing their effective surface areas by introducing nanostructures on the electrode sites. The method combines photolithography and electron-beam evaporation with a locally patterned anodized porous alumina template to integrate Au-nanorod arrays on the flexible thin-film microelectrode, which can significantly increase the effective surface area and decrease impedance due to its 3-D and compact nanostructures. Moreover, the geometrical and electrical properties of Au-nanorod electrodes were demonstrated and compared with conventional planar microelectrodes by using a scanning electron microscope and an impedance spectroscopy system. Experimental results showed that approximately 25 times lower interface impedance was achieved for this nanostructured microelectrode. Such Au-nanorod integrated microelectrode arrays will be a promising tool for neural engineering.