ABSTRACT Natural ventilation micropropagation systems differ from conventional systems by allowing gas exchange between the internal and external media of the culture flask. The objective of this work was to compare the conventional system of in vitro propagation of Eugenia dysenterica (Mart.) DC. with a natural ventilation system. For shooting, explants were inoculated into test tubes with conventional lids and natural ventilation lids (NV), and WPM medium supplemented with four concentrations levels of 6-benzilaminopurine (BAP). The position of explants in each plant was considered by identifying buds as more proximate to the root, or to the apex, or in an intermediate position. Plant growth in the natural ventilation system was superior to that in the conventional system, with a 448.53% increase in leaf number, 85.64% increase in chlorophyll a levels and 74.90% increase in chlorophyll b levels. Plants with intermediate buds exhibited better results. Foliar anatomical analysis revealed abnormalities in leaves grown in the conventional system such as “giant” stomata, which remain always open. Our results indicate that the use of natural ventilation improves the water loss regulation capacity in micropropagated E. dysenterica plants and may favor plants survival and growth after transference to the natural environment.