Global climate change leads to changes in rainfall patterns, making it difficult to predict the occurrence of drought or flooding. Flooding had a negative impact on the rice growth. The objectives of this research were to study growth and aerenchyma formation of rice (Oryza sativa L.) cv. IR64 and Inpara 5 at different inundation conditions. This research was conducted in the greenhouse, Faculty of Biology, UGM from March to December 2012. Experiment design used was completely randomized design with factorial pattern of depth and period of inundation. Depth of inundation consists of 4 levels: T0 = 0 cm, T1 = 4 cm, T2 = 8 cm, and T3 = 12 cm from the soil surface, while the period of inundation consists of 3 levels, i.e. P1 = 10 days inundation on the vegetative phase, P2 = 10 days inundation on the reproductive phase, and P3 = 10 days inundation on the vegetative and reproductive phase. The parameters observed were plant height, flowering time, soluble sugar and starch content in leaf, root anatomical structure. Data analysis was carried out by ANOVA and the differences between treatments were compared using DMRT at significancy level of 95%. The results showed that IR64 and Inpara 5 respond differently to inundation. Depth of inundation had no effect on plant height of both IR64 and Inpara 5, while the inundation period showed a significant effect on plant height of Inpara 5. Inundation at vegetative phase increased plant height of Inpara 5. Both IR64 and Inpara 5, depth of inundation increased number of tillers and root aerenchyma formation, whereas period of inundation had no effect. Inundation treatment caused earlier flowering and stabilized soil pH. Starch content in leaf of Inpara 5 increased with inundation, while in IR64 decreased.