Comparisons of tropospheric carbon monoxide (CO) volume mixing ratio profiles and total columns are presented from nadir-viewing measurements made by the Tropospheric Emission Spectrometer (TES) on the NASA Aura satellite and by the Measurements of Pollution in the Troposphere (MOPITT) instrument on the NASA Terra satellite. In this paper, we first explore the factors that relate the retrieved and the true species profiles. We demonstrate that at a given location and time the retrieved species profiles reported by different satellite instrument teams can be very different from each other. We demonstrate the influence of the a priori data and instrument characteristics on the CO products from TES and MOPITT and on their comparisons. Direct comparison of TES and MOPITT retrieved CO profiles and columns show significant differences in the lower and upper troposphere. To perform a more proper and rigorous comparison between the two instrument observations we allow for different a priori profiles and averaging kernels. We compare (1) TES retrieved CO profiles adjusted to the MOPITT a priori with the MOPITT retrievals and (2) the above adjusted TES CO profiles with the MOPITT profiles vertically smoothed by the TES averaging kernels. These two steps greatly improve the agreement between the CO profiles and the columns from the two instruments. No systematic differences are found as a function of latitude in the final comparisons. These results show that knowledge of the a priori profiles, the averaging kernels, and the error covariance matrices in the standard data products provided by the instrument teams and understanding their roles in the retrieval products are essential in quantitatively interpreting both retrieved profiles and the derived total or partial columns for scientific applications.