Six rice (Oryza sativar L.) varieties (Beodien, KD18, Koshihikari, Sensho, Rayada) were used to evaluate genotypic variation in growth and water use efficiency in the response to different water regimes at seedling stage. Five days after sowing, seedlings were thinned to one plant per pot and water treatments; flooding as a control, well-irrigated (24% Soil moisture content (SMC) (w/w)) and drought (12% SMC) were applied. The results of this experiment indicated that shoot dry weight (SDW), root dry weight (RDW), total dry weight (TDW), leaf area (LA), water use (WU) and water use efficiency (WUE) of Rayada, Sensho, KD18 and IR24 were not significantly different between control and well-irrigated conditions. Those of Koshihikari and Beodien in well-irrigated were lower than those in control. In the aerobic conditions (24% and 12% SMC conditions), total root length (RL), root surface area (RSA) tended to increase in almost varieties except Koshihikari. RL, RSA and root volume (RV) of Koshihikari in the aerobic conditions were lower than those in control. Among varieties used, Rayada had the highest value in RL, RSA, RV, SDW, TDW, LA and WU, followed by Sensho. Moreover, Rayada had also the highest value in WUE in drought conditions, followed by Sensho. Although KD18 and IR24 had lower values in LA, SDW, RDW, TDW, and WU at all treatments, these characters were not severely affected by drought compared with other varieties. The results suggested that Rayada and Sensho are suitable with aerobic rice system and Koshihikari is not adaptable. Indica lowland rice varieties, KD18 and IR24 may be desirable drought tolerant varieties compared with japonica lowland rice variety, Koshihikari.