Nitrate as one of the two main nitrogen source compounds, acts also as a potent signal substance in plant growth and development. It is increasingly interesting to determine whether nitrate itself or the derived metabolites acts as a signal during the regulation. Rice seedlings were treated with different nitrogen forms (NO(-)(3) vs. NH(+)(4)) and total proteins extracted either from nitrate-fed or ammonium-fed leaves were separated by two-dimensional gel electrophoresis (2-DE), and then the differentially-expressed proteins were identified by MALDI-TOF-MS or ESI-Q-TOF-MS. Twenty-six proteins were up-regulated with NO(-)(3) as the nitrogen source while 6 were up-regulated with NH(+)(4) as the nitrogen source. MS analysis, in combination with database searching, allowed for only a total of 11 proteins identified with significant probability. Among them 7 nitrate-up-regulated proteins were identified, i.e., a PSII oxygen-evolving complex protein 1 (N1), a putative CC-NBS-LRR resistance protein MLA13 (N2), a 23-kD polypeptide of PSII (N3), a translation initiation factor eIF-5A (N5), a putative PSII oxygen-evolving complex protein 2 precursor (N8), an unknown protein (N17), and the ubiquitin carrier protein UBC7 (N18). Four ammonium-up-regulated proteins were identified as the ATP synthase beta subunit (A1), the putative aminotransferase (A3), a hypothetical protein (A5), and OSJNBb0032K15.22 (A6). These results give some new insights into both the biochemical adaptation of plant to different nitrogen forms (NO(-)(3)/NH(+)(4)) and the differences in responses signaled by NO(-)(3)/NH(+)(4) in rice.