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ZnO nanorod arrays (ZNAs) were hydrothermally synthesized on the surface of patterned indium-doped tin oxide p-type contact (PIPC) of GaN-based light-emitting diodes (GaN-LEDs) for enhancing the light extraction efficiency (LEE). It was found that the alignment of the ZnO nanorod arrays in the grooves of the PIPC was poorer than these grown on the ridges of the PIPC. By comparing the light output of the GaN-LEDs with and without ZNAs grown in the grooves of PIPC, the influence of the alignment of ZNAs on the LEE of GaN-LEDs was revealed and investigated. Numerical analysis based on the finite difference of time domain (FDTD) method suggested that the poorer alignment of ZNAs grown on GaN-LEDs resulted in more energy reflected back into GaN-LEDs and lower light extraction efficiency.