To assess the impact of the vertical velocity scheme on modeling transport in the tropical tropopause layer (TTL), 3 month backward trajectories are initialized in the TTL for boreal winter and summer 2002. The calculations are done in either a kinematic scenario with pressure tendency as the vertical velocity or in a diabatic scenario with cross-isentropic velocity deduced from various diabatic heating rates due to radiation (clear sky, all sky) and latent, diffusive and turbulent heating. This work provides a guideline for assessing the sensitivity of trajectory and chemical transport model (CTM) results on the choice of the vertical velocity scheme. We find that many transport characteristics, such as time scales, pathways and dispersion, crucially depend on the vertical velocity scheme. The strongest tropical upwelling results from the operational European Centre for Medium-Range Weather Forecasts kinematic scenario with the time scale for ascending from 340 to 400 K of 1 month. For the ERA-Interim kinematic and total diabatic scenarios, this time scale is about 2 months, and for the all-sky scenario it is as long as 2.5 months. In a diabatic scenario, the whole TTL exhibits mean upward motion, whereas in a kinematic scenario, regions of subsidence occur in the upper TTL. However, some transport characteristics robustly emerge from the different scenarios, such as an enhancement of residence times between 350 and 380 K and a strong impact of meridional in-mixing from the extratropics on the composition of the TTL. Moreover, an increase of meridionally transported air from the summer hemisphere into the TTL (maximum for boreal summer) is found as an invariant feature among all the scenarios.