A cloud masking algorithm based on the spatial variability of reflectances at the top of the atmosphere in visible wavelengths was developed for the retrieval of aerosol properties by MODIS. It is shown that the spatial pattern of cloud reflectance as observed from space, is very different from that of aerosols. Clouds show a very high spatial variability in the scale of hundred meters to few kilometers, whereas aerosols in general are very homogeneous. The concept of spatial variability of reflectances at the top of the atmosphere is mainly applicable over the ocean where the surface background is sufficiently homogeneous for the separation between aerosols and clouds. Aerosol retrievals require a particular cloud masking approach since a conservative mask will screen out strong aerosol episodes and a less conservative mask could allow for cloud contamination that tremendously affect the retrieved aerosol optical properties (e.g. aerosol optical depth and effective radii). A detailed study on the effect of cloud contamination on aerosol retrievals is performed and parameters are established determining the threshold value for the MODIS aerosol cloud mask (3X3-STD) over the ocean. The 3X3-STD algorithm discussed in this paper is the operational cloud mask used for MODIS aerosol retrievals over the ocean.