Gene transfer techniques offer an alternative to improve existing cultivars and to obtain new ones. Establishment of tissue culture procedures is a prerequisite in order to obtain stable transformants. However, plants regenerated from tissue culture may exhibit somaclonal variation. These variations, generally undesired, include nucleotide mutations, gene activation/silencing, chromosome abnormalities. Gene silencing and activation occur by DNA methylation and activation of transposable elements. Movement of transposable elements also causes insertional polymorphisms in genome. DNA polymorphisms in 15-day-old, 30-day-old calli and 4-day-old barley (Hordeum vulgare 'Zafer-160') seedling were investigated with Inter-Retrotransposon Amplified Polymorphism (IRAP), a retrotransposon-based marker system. PCR primers designed from BARE-1 and Sukkula elements were combined and amplification products were resolved on non-denaturing polyacrylamide gels. Different polymorphic bands were detected, although banding patterns were highly monomorphic among different tissues. However, control (4-day-old seedling) tissue and 30-day-old callus gave more similar fingerprints.