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We compare differences in ice and liquid water cloud physical and optical properties between Aqua Moderate Resolution Imaging Spectroradiometer (MODIS) collection 6 (C6) and collection 5.1 (C51). The C6 cloud products changed significantly due to improved calibration, improvements based on comparisons with the Cloud-Aerosol Lidar with Orthogonal Polarization, treatment of subpixel liquid water clouds, introduction of a roughened ice habit for C6 rather than the use of smooth ice particles in C51, and more. The MODIS cloud products form a long-term data set for analysis, modeling, and various purposes. Thus, it is important to understand the impact of the changes. Two cases are considered for C6 to C51 comparisons. Case 1 considers pixels with valid cloud retrievals in both C6 and C51, while case 2 compares all valid cloud retrievals in each collection. One year (2012) of level-2 MODIS cloud products are examined, including cloud effective radius (CER), optical thickness (COT), water path, cloud top pressure (CTP), cloud top temperature, and cloud fraction. Large C6–C51 differences are found in the ice CER (regionally, as large as 15 μm) and COT (decrease in annual average by approximately 25%). Liquid water clouds have higher CTP in marine stratocumulus regions in C6 but lower CTP globally ( 5 hPa), and there are 66% more valid pixels in C6 (case 2) due to the treatment of pixels with subpixel clouds. Simulated total cloud radiative signatures from C51 and C6 are compared to Clouds and the Earth’s Radiant Energy System Energy Balanced And Filled (EBAF) product. The C6 CREs compare more closely with the EBAF than the C51 counterparts.