The transcription of plant pathogenesis related (PR) genes were known to be induced by pathogen invasion. Immerging evidences revealed that the transcription of PR genes also up-regulated under abiotic stresses, however, limited data for PR proteins expression was reported. To characterize the expression of rice PR proteins under stresses, we examined the expressions of eight PR proteins under cold, hot, drought, submerge and salt stresses at seedling stage by Western blotting (WB) via antibody-based proteomics strategy. The results showed that the expressions of PR8 was up-regulated under cold stress, the expressions of PR1a, PR3, PR5 and PR16 were down-regulated under hot stress. The expressions of PR1a, PR2 and PR8 were up-regulated while PR5 and PR16 were down-regulated under drought stress, the expressions of PR1, PR2 and PR15 were up-regulated and PR1a, PR3, PR5 and PR8 were down-regulated under submerge stress. The expressions of PR2 and PR3 were up-regulated while PR1a, PR5, PR8 and PR16 were down-regulated under salt stress. In addition, a number of stress responsive cis-elements, such as the ABRE, TC-rich repeats and HSE, were identified in the promoter region of PR genes. These data supported that PR proteins play important and specific roles in the process of stress tolerance.