The blue light photoreceptor mutant cryptochrome1-304 (cry1-304) and Columbia wild-type 4 (col-4) of Arabidopsis thaliana were grown under white light and blue light, and in the dark. To study the difference in protein expression levels between cry1-304 and col-4, a proteomic approach was applied based on 2-D gel electrophoresis. Twenty-one different protein spots were identified by matrix-assisted laser desorption/ionization-time of flight/time of flight mass spectrometry. The expression of four genes corresponding to four protein spots was analyzed by semiquantitative reverse transcription-polymerase chain reaction. We applied analytical procedures to study cry1-304 and col-4, and found that the differentially expressed proteins formed six clusters reflecting co-regulation. This assessment was consistent with the known physiological responses of plants to light.