Retrotransposons are ubiquitous components of genomes especially in cereals. Because of its high retrotransposon content barley is an excellent model plant for retrotransposon studies. BAGY2 is one of the active retrotransposon in barley and it encodes five (gag, protease, reverse transcriptase, ribonuclease H and integrase) proteins needed for its own transposition. It is known that some retrotransposons are activated by tissue culture. To find out whether BAGY2 have a copy number alteration during callus and shoot development we analyzed copy number of BAGY2 internal domains by qPCR in 45- and 90-day-old calli and regenerants deriving from the same embryo. qPCR results were evaluated by One-Way ANOVA. It was found that the copy number of all the domains increased in different tissue culture samples. Further, BAGY2 internal domains were higher in calli samples then shoots. This result shows that the cells which have more stable genome than other cells have more chance for regeneration.