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The Microwave Limb Sounder instrument was launched aboard NASA's EOS AURA satellite in July, 2004. The overall scientific objectives for MLS are to measure temperature, pressure, and several important chemical species in the upper troposphere and stratosphere relevant to ozone processes and climate change. MLS consists of a suite of radiometers designed to operate from 11 8 GHz to 2.5 THz, with two antennas (one for 2.5 THz, the other for the lower frequencies) that scan vertically through the atmospheric limb, and spectrometers with spectral resolution of 6 MHz at spectral line centers. This paper describes the on-orbit commissioning the MLS instrument which includes activation and engineering functional verifications and calibrations.