Group II introns are widespread among plant organellar genomes. Despite several investigations, knowledge about the structural features of group II introns in relation to the possible mechanism of splicing after releasing is still scarce. In the present paper, we have analyzed degradation products of the ndhA, atpF, and petB transcripts, demonstrating the existence of both incomplete introns and unspliced pre-mRNAs, which presumably correspond with their respective intermediate degradation products. Nucleotide sequencing of both 5' and 3' ends of such RNA species showed, for the first time in plant transcripts, that cleavages affect specific intron domains and occur within an unpaired bubble flanked by two-stem structures typical for prokaryotic RNAse III processing sites. Degradation of both unspliced pre-mRNAs and lariat introns is also proposed as an additional mechanism that controls the level of mature translatable mRNAs of chloroplast genes.