Differences in cloud droplet effective radius and cloud droplet number concentration (CDNC) estimates inferred from the Aqua MODIS Collections 5.1 and 6 cloud products (MYD06) are examined for warm clouds over global oceans for the year 2008. Individual pixel level retrievals for both collections are aggregated to 1° × 1° and compared globally and regionally for the three main spectral channel pairs used for MODIS cloud optical property retrievals. Comparisons between both collections are performed for cases in which all three effective radii retrievals are classified by the MODIS Cloud Product as valid. The contribution to the observed differences of several key MYD06 Collection 6 algorithm updates are also explored, with a focus on changes to the surface reflectance model, assumed solar irradiance, above cloud emission, cloud top pressure, and pixel registration. Global results show a neutral to positive (> 50 cm-3) change for C6-derived CDNC relative to C5.1 for the 1.6 µm and 2.1 µm channel retrievals, corresponding to a neutral to -2 µm difference in droplet effective radius. For 3.7 µm retrievals, CDNC results show a negative change in the tropics, with differences transitioning toward positive values with increasing latitude spanning -25 to +50 cm-3 related to a +2.5 to -1 µm transition in effective radius. Cloud optical thickness differences were small relative to effective radius, and found to not significantly impact CDNC estimates. Regionally, the magnitude and behavior of the annual CDNC cycle are compared for each effective radius retrieval. Results from this study indicate significant intercollection differences in aggregated values of effective radius due to changes to the pre-computed retrieval lookup tables for ocean scenes, changes to retrieved cloud top pressure, solar irradiance, or above cloud thermal emission, depending upon spectral channel. The observed differences between collections may have implications for existing MODIS derived climatologies and validation studies of effective radius and CDNC.