Accumulation of unfolded proteins caused by inefficient chaperone activity in the endoplasmic reticulum (ER) is termed 'ER stress', and it is perceived by a complex gene network. Induction of these genes triggers a response termed the 'unfolded protein response' (UPR). If a cell cannot overcome the accumulation of unfolded proteins, the ER-associated degradation (ERAD) system is induced to degrade those proteins. In addition to other factors, reactive oxygen species (ROS) are also produced during oxidative protein-folding in the ER. It has been shown in animal systems that there is a tight association between mitochondrial ROS and ER stress. However, in plants there are no reports concerning how induced ROS production in mitochondria and chloroplasts affects ER stress and if there is a possible role of organelle-originated ROS as a messenger molecule in the unfolded protein response. To address this issue, electron transport in chloroplasts and mitochondria and carnitine acetyl transferase (CAT) activity in peroxisomes were inhibited in wild-type Arabidopsis thaliana to induce ROS production. Expression of UPR genes was then investigated. Plants of A. thaliana ecotype Col-0 were treated with various H2O2- and ROS-producing agents specific to different organelles, including the mitochondria, chloroplasts and peroxisomes. The expression of ER stress sensor/transducer genes (bZIP28, bZIP17, IRE1A, IRE1B, BiP1, BiP3), genes related to protein folding (CNX, ERO1) and ERAD genes (HRD1, SEL1, DER1, UBC32) were evaluated by qRT-PCR analysis. Relatively low concentrations of ROS were more effective for induction of the ER stress response. Mitochondrial and chloroplastic ROS production had different induction mechanisms for the UPR and ER stress responses. Chloroplast- and mitochondria-originated ROS have distinct roles in triggering the ER stress response. In general, low concentrations of ROS induced the transcription of ER stress-related genes, which can be attributed to the roles of ROS as secondary messengers. This is the first time that ROS production in organelles has been shown to affect the ER stress response in a plant system.