Wetlands are common in the Cerrado (Brazilian savannas) biome, however flooding of these wetlands impairs growth and development of most plants. We evaluated flood tolerance of typical Cerrado trees. Seedlings of Aspidosperma macrocarpon (Apocynaceae), Tabebuia rosea (Bignoniaceae), Handroanthus chrysotrichus (Bignoniaceae), Myracrodruon urundeuva (Anacardiaceae), Kielmeyera coriacea (Calophyllaceae) and Copaifera langsdorffii (Fabaceae) were flooded up to the stem base for 30 days. Stems with cortical cracks, secondary aerenchyma and hypertrophic lenticels were observed in flooded plants of M. urundeuva,H. chrysotrichus and T. rosea while adventitious roots were formed in flooded plants of T. rosea and H. chrysotrichus. However, only T. rosea developed aerenchyma in the root cortex. K. coriacea and A. macrocarpon were the most sensitive to flooding, showing a decrease in survival and necrosis of the leaves and roots. C. langsdorffii and M. urundeuva were less sensitive to flooding, although reductions in root biomass and symptoms of necrosis of the roots were noticeable in flooded seedlings. Flooded M. urundeuva seedlings also had a decrease in total leaf area, leaf biomass, total biomass and in stem growth. Flooding affected root development and reduced stem growth of H. chrysotrichus with symptoms of necrosis of the leaves and roots. T. rosea was the only species where symptoms of injury from flooding were not evident.