The consistency of cloud top temperature (TC) and effective cloud fraction ( f ) retrieved by the Atmospheric Infrared Sounder (AIRS)/Advanced Microwave Sounding Unit (AMSU) observation suite and the Moderate Resolution Imaging Spectroradiometer (MODIS) on the EOS-Aqua platform are investigated. Collocated AIRS and MODIS TC and f are compared via an ‘‘effective scene brightness temperature’’ (Tb,e). Tb,e is calculated with partial field of view (FOV) contributions from TC and surface temperature (TS), weighted by f and 1Àf, respectively. AIRS reports up to two cloud layers while MODIS reports up to one. However, MODIS reports TC, TS, and f at a higher spatial resolution than AIRS. As a result, pixel-scale comparisons of TC and f are difficult to interpret, demonstrating the need for alternatives such as Tb,e. AIRS-MODIS Tb,e differences (DTb,e) for identical observing scenes are useful as a diagnostic for cloud quantity comparisons. The smallest values of DTb,e are for high and opaque clouds, with increasing scatter in DTb,e for clouds of smaller opacity and lower altitude. A persistent positive bias in DTb,e is observed in warmer and low-latitude scenes, characterized by a mixture of MODIS CO2 slicing and 11-mm window retrievals. These scenes contain heterogeneous cloud cover, including mixtures of multilayered cloudiness and misplaced MODIS cloud top pressure. The spatial patterns of DTb,e are systematic and do not correlate well with collocated AIRS-MODIS radiance differences, which are more random in nature and smaller in magnitude than DTb,e. This suggests that the observed inconsistencies in AIRS and MODIS cloud fields are dominated by retrieval algorithm differences, instead of differences in the observed radiances. The results presented here have implications for the validation of cloudy satellite retrieval algorithms, and use of cloud products in quantitative analyses.