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RNA quality is directly correlated to the success of various applications, such as microarray or real time qPCR-based gene expression analyses, cDNA library construction, Northern analyses, and RNAse protection assays, which utilize RNA samples from various organisms, tissues, cell lines, and precious biological samples. We present a novel method for examining RNA integrity and purity using capillary electrophoresis that is more cost-effective and scalable than current standard methods. This highly sensitive method uses less material, uncovers impurities following RNA purification, and detects degradation resulting from nuclease contamination. Total RNA and cRNA, derived from various tissues and cell lines, were stained with the dye YOYO-1 and run through a custom polymer formulation on a capillary electrophoresis platform. Using downstream analysis software, we resolved RNA species and their relative quality based on parameters such as size, profile, peak area, and peak height. Our results highlight the potential for high-throughput capillary electrophoresis as a much more discriminatory and cost-saving method in evaluating RNA quality.