To gain a better understanding of the mechanism of rice (Oryza sativa L.) in response to salt stress, we performed a proteomics analysis of rice in response to 250 mM NaCl treatment using shoots of 3-day-old nascent seedlings. The changes of protein patterns were monitored with two-dimensional gel electrophoresis. Of 57 protein spots showing changes in abundance in response to salt stress, 52 were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The identified proteins were classified into eight functional categories. Several novel salt stress-responsive proteins, including protein synthesis inhibitor I, photosystem II stability/assembly factor HCF136, trigger factor-like protein and cycloartenol-C24-methyltransferase are upregulated upon salt stress. In order to figure out the different and similar molecular mechanism among salt and other stresses, regulation of some salt responsive proteins under other abiotic stress (cold and dehydration) and abscisic acid application was also analyzed. The possible molecular mechanism of rice seedlings in response to salinity and other stresses were discussed.