Immune systems are fundamentally based on the differentiation of self and non-self. Unlike mammals, plants have an innate immune system responding to the pathogen only at the site of attack. One of these pathogens is Blumeria graminis f. sp. hordei which is an obligate biotrophic pathogen causing powdery mildew disease and resulting in up to 30% yield loss for both cultivated and wild barley. In this study, Pallas-01 (P-01) and Pallas-03 (P-03) barley lines were inoculated with powdery mildew race Bgh103 (64/01) resulting incompatible and compatible interactions, respectively. 6, 12, 24, 48 and 72 hour-post-inoculation (hpi) samples were used in order to define the differential gene expression of NAD malic enzyme, chloroplast lipocalin, phosphoglyceromutase (PGM), Mg chelatase and 26S protease regulatory subunit 6B homolog. In the proteomics study previously conducted in the laboratory, except for the NAD-dependent malic enzyme, the other four proteins were shown to be involved in the incompatible interaction of P-01 and Bgh103 at protein level, whereas NAD-dependent malic enzyme was changing in the compatible interaction. The expression level for both proteomics and transcriptomics were assumed to be similar. However, the level of transcript would not always reflect its protein level or correlate with the level of proteins, due to complex cellular regulation processes. Post-transcriptional modifications such as synthesis, processing, degradation and post-translational modifications are changing the level of proteins expressed, thus a parallel correlation between the protein and mRNA levels can be lost. Other possible reasons for this variation can be changes in mRNA and protein stability, efficiency of translation and protein&rsquo / s turnover rate. The transcription level changes of the genes investigated in this study are found to be differentially expressed, supporting the proteomics data indicating that these genes are possibly involved in resistance. For further investigations, genetic tools such as gene silencing with RNAi and knockout experiments are required in order to elucidate the mechanism of these candidate genes in the plant-pathogen interaction.