The role of clouds in modulating vertically integrated atmospheric heating is investigated using CloudSat’s multisensor radiative flux dataset. On the global mean, clouds are found to induce a net atmospheric heating of 0.07 ± 0.08 K day−1 that derives largely from 0.06 ± 0.07 K day−1 of enhanced shortwave absorption and a small, 0.01 ± 0.04 K day−1 reduction of longwave cooling. However, this small global average longwave effect results from the near cancellation of much larger regional warming by multilayered cloud systems in the tropics and cooling from stratocumulus clouds in subtropical oceans. Clouds are observed to warm the tropical atmosphere by 0.23 K day−1 and cool the polar atmosphere by −0.13 K day−1 enhancing required zonal heat redistribution by the meridional overturning circulation. Zonal asymmetries in the occurrence of multilayered clouds that are more frequent in the Northern Hemisphere and stratocumulus that occur more frequently over the southern oceans also leads to 3 times as much cloud heating in the Northern Hemisphere (0.1 K day−1) than the Southern Hemisphere (0.04 K day−1). These findings suggest that clouds very likely make the strongest contribution to the annual mean atmospheric energy imbalance between the hemispheres (2.0 ± 3.5 PW).