Vertical stratification of vascular epiphytes is frequently attributed to niche partitioning along microclimatic gradients but experimental confirmations of this notion are rare. This study investigates the role of the regeneration phase for the stratification of five bromeliad (Catopsis sessiliflora, Guzmania subcorymbosa, Tillandsia anceps, T. bulbosa and Werauhia gladioliflora) and seven aroid species (Anthurium acutangulum, A. brownii, A. clavigerum, A. durandii, A. friedrichsthalii, A. hacumense and A. scandens) in a Panamanian rain forest. We documented gradients of temperature, vapour pressure deficit and light (n = 10 d) as well as species height distributions (n = 11–120). Microclimatic gradients were substantial (maximal T and RH differences between strata: 5 °C and 18%, respectively) and mean attachment heights of the study species (range = 4–21 m) differed significantly. We tested sensitivity to recurrent drought (four treatments) during germination (all species, cumulative germination of 20 seeds, n = 3) and seedling growth (four aroid species, n = 25). Seedling survival of six aroid species transplanted to three heights (n = 27) was monitored in situ. Some species did not germinate under severe recurrent drought while others germinated at the same rate in all treatments. Seedlings of the most exposed species grew fastest under intermediate recurrent drought while those of the other three species grew fastest when kept constantly wet. Survival of transplanted seedlings did not depend on species attachment height, but this may be attributable to insufficient statistical power. Taken together, the results suggest that the stratification can be explained to a large degree by differential sensitivity to the vertical moisture gradient during the regeneration phase.