Many crops are sensitive to waterlogging. A small, fast-growing grass, Brachypodium distachyon (Bd21), whose genome has been sequenced, is a new model for studying cereal crops such as wheat and barley, and for developing novel biomass grasses. However, its waterlogging tolerance and oxygen transport properties are not known. Here, we show that in stagnant deoxygenated nutrient solution, which mimics waterlogged soil, B. distachyon grows poorly and does not increase the number of newly formed roots. In both aerated and stagnant conditions, aerenchyma was hardly observed in roots, and root porosities were low. Suberin and lignin, which are thought to be constituents of Casparian strips and the barrier to radial oxygen loss, did not develop in the outer part of roots in either aerated or stagnant conditions. Our results suggest that the abilities of oxygen transport in B. distachyon are insufficient to grow and survive in stagnant deoxygenated conditions.