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Experiments in engine test cells are under the influence of several parameters and types of equipment, which may impact the test results. Many variables of interest are derived from the combination of more than one quantity, increasing the results uncertainty of the final reported value. This paper describes a detailed procedure to calculate uncertainty of measurement of emission tests using a FTIR (Fourrier Transformed Infrared) emission analyzer. A Flex-Fuel engine using gasoline and ethanol was tested under different operating conditions on an engine dynamometer equipped with automation system. For each operating condition at least four different measurements were taken. The expanded uncertainty was calculated by the combination of Type A (due to repeatability) and Type B (due to calibration, sensor resolution and others).