The active transcription of some plant retrotransposons under diverse stress conditions suggests active transposition. However, transposition has been demonstrated only during tissue/cell culture. To examine whether transposition is activated under conditions other than tissue/cell culture, DNA intermediates for retrotransposition of the tobacco retrotransposon Tto1 were analysed. Using transgenic Arabidopsis callus expressing high levels of Tto1 RNA in a ddm1 hypomethylation mutant background, the existence of extrachromosomal Tto1 linear DNA molecules in a Gag-particle fraction was demonstrated. By combination with ligation-mediated PCR amplification, we detected Tto1 linear DNA molecules in particle fractions from callus and methyl jasmonate-treated leaves of tobacco, but not from non-stressed leaves. Tto1 DNA intermediates could not be detected in the tobacco corolla where Tto1 is expressed. These results indicate that the transcriptional activation of Tto1 by defence-related stresses leads to the synthesis of DNA intermediates, whereas post-transcriptional suppression of Tto1 activity is suggested in the corolla.