Abstract Human frozen tissues are one of the best sources for molecular analyses such as microarrays, qPCR or Next-Generation-Sequencing. In addition, frozen tissues are particularly valuable for biomarker identification. Several biobanks comprising non-fixed frozen tissues have been established alongside with corresponding clinical data repositories to facilitate biomarker studies relevant for clinical diagnostics. Apart from proteomic approaches, mRNA- and microRNA-expression profiles have shown to be highly valuable for biomarker studies. Since RNA is generally a fragile molecule, RNA integrity in tissue specimens has tremendous impact on gene expression analyses, requiring a rigorous quality assessment of biobank tissue samples. To address this issue, we established a tissue quality test system based on RNA integrity and differential gene expression. We used normal liver tissue, that was snap frozen after various periods of ischemia time. The RNA was isolated and the quality was assessed in four steps: First, the RNA was quantitated by spectrophotometry (NanoDrop) and total RNA quality was determined by on-chip electrophoresis (Experion). Second, the degree of RNA degradation and the maximum length of RNA molecules available for downstream applications was determined by amplicon length analysis using PCR amplification. Third, the RNA expression levels of selected genes were determined and correlated to the time and condition of ischemia. The genes analysed comprised highly regulated genes, signaling pathway genes and genes induced by hypoxia or apoptosis. Fourth, the expression of selected miRNAs involved in signaling pathway regulation was determined by quantitative PCR. Taken together we analysed mRNA and miRNA stability in correlation to the time of warm and cold ischemia and its impact on signaling pathway regulation in liver tissue samples. The results enabled us to establish a RNA-based quality assessment procedure of tissue specimen for frozen tissue biobanks. This study may facilitate and optimise the logistics of biobanking processes. Citation Format: Claudia Schuster, Wolfgang E. Thasler, Thomas Kirchner, Falk Hlubek. Impact of ischemia time on mRNA and microRNA expression in surgical liver tissue. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1795. doi:10.1158/1538-7445.AM2013-1795