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The impact of horizontal heterogeneities, liquid water path (LWP from AMSR-E), and cloud fraction (CF) on MODIS cloud effective radius (re ), retrieved from the 2.1 µm (re2.1 ) and 3.8 µm (re3.8 ) channels, is investigated for warm clouds over the southeast Pacific. Values of re retrieved using the CERES algorithms are averaged at the CERES footprint resolution (∼ 20 km), while heterogeneities (Hσ ) are calculated as the ratio between the standard deviation and mean 0.64 µm reflectance. The value of re2.1 strongly depends on CF, with magnitudes up to 5 µm larger than those for overcast scenes, whereas re3.8 remains insensitive to CF. For cloudy scenes, both re2.1 and re3.8 increase with Hσ for any given AMSR-E LWP, but re2.1 changes more than for re3.8 . Additionally, re3.8 –re2.1 differences are positive (< 1 µm) for homogeneous scenes (Hσ < 0.2) and LWP > 45 gm−2 , and negative (up to −4 µm) for larger Hσ . While re3.8 –re2.1 differences in homogeneous scenes are qualitatively consistent with in situ microphysical observations over the region of study, negative differences – particularly evinced in mean regional maps – are more likely to reflect the dominant bias associated with cloud heterogeneities rather than information about the cloud vertical structure. The consequences for MODIS LWP are also discussed.