Increasing world population needs to enhance agricultural production because of food starvation. Genetically modified organism (GMO) is a way to solve this problem. During gene transfers, DNA is inserted into a plant’s genome in a random way. This producesspontaneous genetic changes with movement of transposable elements, and even increases variations. Houba was described as one o f the active retr otransposonsin rice. The aim of this study was to screen rice samples collected from Turkey, and analyse Houba retrotransposon movements with IRAP technique in transgenic ones and their controls. For this purpose, 71 different rice seeds obtained from different regions of Turkey were used for GMO analysis. All samples were screened by real time PCR to test cauliflower mosaic virus (CaMV) 35S promoter (P-35S) regions, T-NOS (nopaline synthase terminator) regions, figwort mosaic virus (FMV) regions, bar, pat and Cry1ab/ac,and hpt (hygromycin resistance) genes. Hpt gene was identified in 6samples as a result of real time PCR an al ys is . These 6 transgenic samples with their controls were used for IRAP-PCRanalysis and 0-56% polymorphism ratios were observed in analysed samples. This study is one of the first detailed experimental data of transgenic Oryza sativa L. samples in terms of retrotransposon-based variation.