Two rice varieties, one perchlorate-tolerant (Gannuoxiang, GN) and the other perchlorate-sensitive (IR65598-112-2, IR), were exposed to 20, 200, and 400 mg/kg soil perchlorate to investigate their physiological responses and perchlorate accumulation. It was found that perchlorate decreased leaf chlorophyll content in both rice varieties. The activities of superoxide dismutase (SOD) and catalase (CAT) decreased while peroxidase (POD) increased in both rice varieties under perchlorate stress at tillering stage. Rice variety IR showed earlier physiological response and was more affected by perchlorate than GN. Perchlorate induced physiological response in different ways depending on perchlorate contamination level, rice variety, and growing stage. Perchlorate concentration in leaves was significantly higher than that in roots, stems and seeds. Perchlorate accumulation in IR leaves was higher than GN, but GN stored more perchlorate in its edible portion at low perchlorate level. These results indicated that high sensitivity of the rice variety IR to perchlorate stress might be due to antioxidant enzymes in perchlorate-detoxification and its higher perchlorate accumulation in leaves.