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Abstract: Dehydration is a necessary procedure prior to exposing seeds to long term storage, but this is associated with metabolism-linked injury mediated by cell injury. In order to assess cellular alterations during re-establishment of desiccation tolerance (DT) in C. fissilis germinated seeds and their relation to DNA damage, we verified the occurrence of DNA fragmentation through the TUNEL test and its evidence through the cytological analyses. To re-establish DT, germinated seeds were incubated for 72 h in polyethylene glycol (PEG, -2.04 MPa) before dehydration in silica gel (at 10% moisture content) followed by rehydration. The moisture content changes during the reestablishment of the desiccation tolerance was accomplished. (DT)TdT-dUPT terminal nick-end labeling (TUNEL) was used to assess rates of cell death. TUNEL staining was performed using Click-iT-TUNEL Alexa Flour imaging assay. The TUNEL test showed a consistent DNA fragmentation in the 2 and 5 mm long radicles. Moreover, nuclear and chromosomal alterations were observed in the 5 mm meristematic root cell cycle, contributing to the identification of diagnostic markers of cell death.