Depending on light access plants use two distinct developmental programs. Dark-grown plants invest stored nutrients on stem elongation (skotomorphogenesis) while under light conditions development of the photosynthetic apparatus is supported (photomorphogenesis). Cytokinins (CKs) can partially replace effect of light in a transition from skototo photomorphogenesis. We investigated, at the proteome level, the transition induced in Arabidopsis dark-grown seedlings by increased levels of endogenous CKs achieved using a pOp-ipt/LhGR system. Total seedling proteins were separated by two-dimensional electrophoresis. Image analysis revealed spots that differed significantly between controls and seedlings with increased CK levels. Candidate proteins were identified by both MALDI-MS and LC-MS/MS. Chloroplast and nuclear proteins represent two major groups in the candidates. A number of them might be involved in chloroplast maturation induced by increased levels of endogenous CKs in the dark grown seedlings. The relevance of the candidate proteins in the CK induced transition from skototo photomorphogenesis will be determined in subsequent experiments. (Supported by grants MSM143100008, MSM0021622415, FRVŠ 804/2005, IAA600380507 and AVOZ50040507.)