The Atmospheric Infrared Sounder (AIRS) is a grating array spectrometer on the EOS Aqua satellite. AIRS covers the thermal infrared spectral range between 640 and 2700 cm-1. In order to retain the maximum radiometric accuracy of the AIRS data, the effects of cloud contamination have to be minimized. We discuss cloud filtering which uses the high spectral resolution of AIRS to identify about 100,000 of 500,000 non-polar ocean spectra per day as relatively free of clouds. The comparison of AIRS surface sensitive channels with the NCEP provided global real time sst (rtg.sst) shows a cold bias of the order of 0.5K in daily global averages, which is traceable to cloud contamination. During the day the cloud contamination is due to a 2-3% broken cloud cover at 1-2 km altitude, characteristic of low stratus clouds. Cloud contamination can be reduced to 0.2K, but not eliminated, by combining the spectral filter with a spatial coherence threshold, but the yield drops to 16,000 spectra per day. AIRS was launched in May 2002 on the Earth Observing System (EOS) Aqua satellite. Since September 2002 it has returned 4 million spectra of the globe each day.