Investigation of operating parameters have been carried out for an FTIR system dedicated for emission analysis. Discussions are focused on the key parameters, such as spectral resolution, gas cell dimensions, quantification algorithm, and sample gas treatment. The spectral resolution has to be determined so that the scan rate is high enough to make transient analysis, the minimum detection limit is low enough to carry out high sensitivity measurement, and no cross sensitivity can be recognized. A trade-off relationship between the response and the sensitivity exists for the gas cell design. Small volume of the cell is desirable when gas replacement is considered. On the other hand, the sensitivity can be increased by enlarging the cell volume to obtain long optical path. Both quantification algorithm and the sample gas treatment have to be well arranged to obtain accurate concentration values of the gas compounds sampled from the tailpipe. An optimized FTIR emission analyzer has been built and the acquired data for unregulated components are shown for gasoline, Diesel, and CNG fueled vehicles with high response and high accuracy. An updated understanding of the technique is also discussed.