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The influence of polarity during the MOVPE growth of GaN based sub-micrometer (sub-μm) rods has mostly been neglected up to now. In this paper we demonstrate that the surface polarity plays a crucial role for the morphology of the GaN sub-μm rods. Based on the differences between N-polar and Ga-polar surfaces, a model is suggested to explain the influence of various parameters on the morphology of GaN sub-μm rods for the first time. For Ga-polar GaN, the {10−11} r-planes, similar to N-polar (000−1) c-planes, are terminated by nitrogen atoms. These N-terminated surfaces can be passivated by hydrogen, which leads to a stable surface with low growth rates and therefore tends to keep a pyramidal shape with stable r-planes. For N-polar GaN, {10−1−1} r-planes can be modified by H2 etching, leading to the formation of more stable {1−100} m-planes, hence supporting the formation of sub-μm rods with vertical sidewalls.