We use radiative transfer calculations to quantify vertical mass transport in the equatorial upper troposphere (UT) and lower stratosphere (LS), employing high resolution sonde measurements of temperature, ozone and water vapor at seven equatorial locations (10°S–10°N). The influence of clouds is examined using data from the International Satellite Cloud Climatology Project (ISCCP) and the Lidar-In-Space Technology Experiment (LITE). The resulting mean heating rate profiles show that the transition from radiative cooling to heating occurs significantly lower in the full sky case than in the clear sky case, demonstrating the importance of clouds for processes in the UT, such as troposphere-to-stratosphere transport (TST). The heating rate profiles are used to calculate mean vertical mass fluxes, which show a divergent mass flux from 15–19 km. This suggests that only a small part of the air ascending through the cold point tropopause can reach the middle stratosphere. Above 19 km the vertical motion is a non-divergent upwelling mass flux consistent with the idea of a Brewer-Dobson circulation driven by waves dissipating in the extratropical stratosphere. Lower down, other processes are also responsible for the upwelling.