Retrotransposons are genetic elements that can move within the genome. They can cause mutations by inserting themselves near or within genes. They may also have an important role in the regulation of the development. Barley is an important model plant in addition to its commercial importance. Retrotransposons constitute more than 50 % of the barley (Hordeum vulgare L.) genome. In this study, we used mature embryo, leaf and root tissues grown from the same barley plant, to investigate BARE1 and BAGY2 retrotransposon movements, and to analyze the expression of inner domains of BARE1-gag, BAGY2-env (envelope) and rt (reverse transcriptase), using IRAP (Inter-Retrotransposon Amplified Polymorphism) and reverse transcriptase PCR (RT-PCR) techniques, respectively. Barley seeds germinated in Petri dishes under sterile conditions for 16 h were used for mature embryo dissection and genomic DNA isolation. Genomic DNA was also isolated from the leaves and roots of 5 individual seedlings which were harvested on the 10th day of germination. IRAP-PCR was performed with each DNA template for BARE1 and BAGY2 retrotransposons. BAGY2 was found to be more stable, while BARE1 polymorphisms were observed among embryos, 10-day-old roots and 10-day-old leaves. We found 50 % similarity between the roots and the leaves, 55 % between the embryo and the roots, and 66 % between the embryo and the leaves.