Coincident MISR and MODIS cloud-top heights retrieved above two vertically pointing radar sites (ARM-SGP and UK-CFARR) are compared for 54 scenes between March 2000 and October 2003. The difference between MODIS and MISR cloud-top heights is assessed in situations where multiple cloud layers are present in a vertical column (i.e., cloud overlap or multilayered cloud). MISR stereo cloud-top heights are known to be sensitive to low-level clouds of high contrast (between two camera views) even if high clouds with a wide range of optical thicknesses are also present in the scene. MODIS retrieved cloud-top heights do not experience this problem as long as the highest cloud layer has a visible optical thickness greater than approximately 1. Consequently, the difference in cloud-top heights between MODIS and MISR is often large and positive in cloud overlap conditions. In cloud overlap conditions, small differences between MODIS and MISR cloud-top heights can be found where both instruments detect the highest cloud layer or, on the contrary, where they both fail to detect the highest cloud but instead detect some lower level cloud. The comparison with radar cloud-top heights on a 21-scene subset confirmed that large differences are associated with cloud overlap, but also showed that small differences can be found in similar situations if the highest layer is of large contrast (both instruments detect the highest cloud layer) or of extremely small optical thickness (both instruments fail to detect the highest cloud layer). With the use of a cloud-typing technique applied to MODIS data that can also identify areas containing cloud overlap, small differences were found to occur for 60-70% of all overlap pixels examined here, highlighting the weakness of using the MODIS-MISR cloud-top height differences as a sole indicator for automated cloud overlap detection. While the accuracy of the MODIS cloud-top pressure/height algorithm decreases as the cirrus optical thickness becomes less than 1, the MISR approach may still be able to infer an accurate cloud-top height depending on the cloud contrast between two view angles. However, synergy between the difference in MODIS-MISR cloud-top height analysis and the MODIS cloud-typing method could improve overlap detection for thin cirrus over low cloud situations and provide additional information on the cloud-top height of two distinct layers.