CO2 migration is affected by rock heterogeneity but is not reflected in the relative permeability (𝑘𝑟(𝑆𝑤)) and capillary pressure (𝑃𝑐(𝑆𝑤)) saturation functions measured by special core analysis (SCAL). We present a first step to an upscaling workflow that combines state-of-the-art SCAL interpretations with continuum-scale experiments on the next larger scale where heterogeneities dictate CO2-brine displacement. By numerical interpretation using 1D homogeneous and 3D heterogeneous simulation domains, we show that an effectively upscaled 𝑘𝑟(𝑆𝑤) is substantially out of the uncertainty range of classical SCAL measurements used for 𝑘𝑟(𝑆𝑤) quantification. Alternatively, by including porosity, permeability and capillary heterogeneity, the SCAL-derived relative permeability is well applied. However, this effectively corresponds to downscaling and is therefore of little value for reservoir simulations. Our results demonstrate the following: (a) simple USS experiments can be used to investigate the influence of capillary heterogeneity on 𝑘𝑟(𝑆𝑤), and (b) a rigorous upscaling procedure including rock heterogeneity on various scales is needed to use standard workflows such as special core analysis for CCS developments in carbonates.