Proper modeling of the multiphase flow of supercritical CO2 in deep saline aquifers for CO2 sequestration (both cycles of drainage during injection and imbibition during CO2 migration) is critical in being able to understand and predict both the short and long term fate of the injected CO2 over extended time periods (hundreds to thousands of years). Current numerical models require the use of accurate two-phase CO2/brine relative permeability data at representative in-situ conditions in order to be able to accurately conduct these calculations. However, there are virtually no published data in the literature on the high temperature and pressure displacement character of CO2/brine systems in actual reservoir rocks, except for the data published by the authors in the June 2008 issue of the SPE Reservoir Evaluation and Engineering Journal. That data set, although it included a few carbonate cases, contained mostly measurements on clastic rocks. This paper presents a new set of nine relative permeability measurements (both drainage and imbibition) for carbonate rocks (limestone and dolomite) of higher permeability values than those in the initial work (which are thus more likely to be representative for candidates for CO2 sequestration in deep saline aquifers). The new data set to be presented includes also pre and post-test CAT-scan imaging of selected samples to illustrate potential effects of CO2 contact on potentially soluble carbonate matrices. The paper compares the new data set of measurements for carbonate rocks with the limited set of data available for carbonates from the previous work, and attempts to determine if specific relative permeability and residual saturation trends can be defined based on other rock characteristics that are easier to measure in routine core analyses, to allow extension of the data set to other carbonate facies elsewhere which have not been tested.