Abstract: In plant, chlorophyll-deficient mutants have been employed to study the mechanism of chlorophyll and chloroplast biogenesis. Here, we found a new chlorophyll-deficient mutant rice line (W02S) whose leaves became etiolated at two-leaf stage and turned into green at three-leaf stage different from that of its isogenic rice line (Peiai64S). Compared with Peiai64S, 44 differentially-expressed proteins were selected in the two-leaf stage of W02S by the means of 2-D gel electrophoresis and MALDI-TOF MS analysis. Among the identified ten categories, four highly expressed protein spots involved in the EMP-TCA pathway and protein expressions were selected for real-time quantitative PCR analysis. The mRNA levels of three genes encoding an enolase, a chloroplast 29 kDa ribonucleoprotein and a proteasome alpha subunit were significantly increased in the two-leaf-stage W02S, indicating that a substantial proportion of protein changes is the consequence of altered mRNA levels during the seedling stages of the mutant rice. These new findings lead us to better understand regulatory mechanisms of chlorophyll-deficient phenotype in rice and other plants.