Cold stress response is extensively studied process in plants. However most studies explore only limited set of organs and developmental stages (leaves or seedlings). In order to gain insight into organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+4ÂºC) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq. It showed that gene expression is highly organ-specific. The results on differential expression in leaves are congruent with current knowledge on stress response pathways, in particular, the role of CBF genes. In other organs, both essence and dynamics of gene expression changes are different. We show the involvement of genes that are confined to narrow expression patterns in non-stress conditions into stress response. In particular, the genes that control cell wall modification in pollen, are activated in leaves. In seeds, predominant pattern is the change of lipid metabolism. We found that stress response is highly organ-specific and highlighted the processes that are involved in this process in each type of organs.