Until few years ago there were limited options of apple rootstocks commercially available for Brazilian growers; although, new series of Geneva® rootstocks introduced recently present desirable features such as vigor control and wider lateral branch angle. On the main apple producing regions of Brazil, intermittent rainfall eventually occurs and waterlogged condition is frequent especially in high clay oxisols; in addition, little is known about the tolerance of rootstocks M.9, Marubakaido/M.9 interstock, G.202, G.213 and G.814 to waterlogging. Thus, the objective of this experiment was to evaluate the tolerance of these rootstocks to short-term waterlogging on root and aerial parameters. Potted ‘Maxi Gala’ apple plants were kept under 48 hours of waterlogging weekly throughout 19 weeks to be compared with a normal hydric condition control. The evaluated variables were: leaf, stem and root dry matter, number and length of new root emission, and number of leaves, mean leaf size and chlorophyll content. Rootstocks G.202, G.814 and Marubakaido/M.9 interstock presented more tolerance to waterlogging, and the main defense mechanism was the emission of new adventitious roots.