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Programmed cell death (PCD) may be triggered by a variety of environmental stimuli. In this report we show that low temperature treatment of tobacco BY-2 cells results in specific chromatin changes. The early stage was characterised by chromatin condensation associated with specific endonucleolytic cleavage of the genome into fragments of 50–100 kbp in size. Later, after 2 weeks of the cold treatment, a ladder of nucleosomal units (178 bp) and their multiples occurred. Chromatin changes were accompanied by a general decrease in cell viability. However, the cell culture retained about 11% of living cells even after prolonged incubation in the cold suggesting the presence of a cold-resistant population of cells. The results support the view that PCD was activated by the cold stress. We suggest that cold-stressed tobacco BY-2 culture might be a useful system for investigation of PCD in plant cells.