Boron, is a microelement that plays a role in plant development. In contrast, excess amount of boron is toxic for plants. Turkey is the second country that has the largest boron reserve in the world, thus boron is one of the major problems in agriculture in Turkey. Barley (Hordeum vulgare) is the second widely produced cereal after wheat. Because barley is used in human diet, animal feeding and beer industry it is an economically valuable crop. There are ten different barley varieties in Turkey and these varieties show different genetic variations against boron toxicity. In this study, Hamidiye (boron sensitive) and Anadolu (boron tolerant) varieties were used to identify genes responsible for boron tolerance. RT-PCR and mRNA Differential Display techniques were used from root and leaf samples of Hamidiye and Anadolu varieties grown in laboratory with or without boron conditions. Eight differentially expressed genes identified by using mRNA Differential Display technique. Sequence of these genes gave homology to an eukaryotic translation initiation factor in Arabidopsis thaliana, a chlorophyll a/b binding protein precursor in Triticum aestivum, an elongation factor in Oryza sativa, short-chain dehydrogenase/reductase family protein in Arabidopsis thaliana, a thioredoxin h isoform in Triticum aestivum, a shaggy-like kinase protein in Triticum aestivum, chloroplast genome in Hordeum vulgare, a hypothetical protein in Arabidopsis thaliana. Expression level of six of forty three antiporter genes showed differences between Anadolu and Hamidiye cultivars in Real Time PCR.