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Observations of the aerosol optical thickness (AOT) by the Moderate Resolution Imaging Spectroradiometer (MODIS) instruments aboard Terra and Aqua satellites are being used extensively for applications to climate and air quality studies. Data quality is essential for these studies. Here we investigate the effects of unresolved clouds on the MODIS measurements of the AOT. The main cloud effect is from residual cirrus that increases the AOT by 0.015±0.003 at 0.55 μm. In addition, lower level clouds can add contamination. We examine the effect of lower clouds using the difference between simultaneously measured MODIS and AERONET AOT. The difference is positively correlated with the cloud fraction. However, interpretation of this difference is sensitive to the definition of cloud contamination versus aerosol growth. If we consider this consistent difference between MODIS and AERONET to be entirely due to cloud contamination we get a total cloud contamination of 0.025±0.005, though a more likely estimate is closer to 0.020 after accounting for aerosol growth. This reduces the difference between MODIS-observed global aerosol optical thickness over the oceans and model simulations by half, from 0.04 to 0.02. However it is insignificant for studies of aerosol cloud interaction. We also examined how representative are the MODIS data of the diurnal average aerosol. Comparison to monthly averaged sunphotometer data confirms that either the Terra or Aqua estimate of global AOT is a valid representation of the daily average. Though in the vicinity of aerosol sources such as fires, we do not expect this to be true.