Proline accumulation is a common physiological response to various abiotic stresses in plants. In this study, we show that rice seedlings accumulate proline to different levels in response to different saline-alkaline stress factors including osmotic, saline and alkaline stresses. Expression analysis of genes for proline biosynthesis (OsP5CS1, OsP5CS2 and OsP5CR) and catabolism (OsPDH1 and OsP5CDH) revealed up-regulation of the proline synthesis genes under osmotic and alkaline stresses. In comparison, under the salt stress, a decrease in catabolic enzyme gene expressions was observed. Our results suggest that rice seedlings employ different gene regulation in proline accumulation in response to different saline-alkaline stress factors.