Technical Abstract: Bovine viral diarrhea viruses (BVDV) are significant pathogens of cattle worldwide. These viruses exist in both non-cytopathic and cytopathic biotypes. Non-cytopathic BVDV can establish persistent lifelong infections in cattle and are a frequent contaminant of biological reagents such as cell cultures and fetal bovine serum. We identified commercially available bovine aortic endothelial cells (BAEC) were contaminated with BVDV. To determine if BVDV alters endothelial gene transcription patterns, we used serial analysis of gene expression (SAGE) to compare gene expression profiles from uninfected and BVDV contaminated BAEC. SAGE is an open ended, quantitative method for characterizing global patterns of transcription. Comparison of expression profiles of BVDV-contaminated and noninfected cells revealed significant increases in the transcription of many genes including P-selectin, tryptophan tRNA synthetase and prostaglandin D2 synthase. These changes were validated by real-time PCR. Additionally, real-time PCR demonstrated that the response to LPS and dsRNA by contaminated cells, as well as cells acutely infected with noncytopathic BVDV, is altered. The altered response may be through the high level of expression of A20 and inhibition of activation of NF-kappaB. BAEC are commonly used as a model to study endothelial cell function in many different systems. As shown here, transcriptional, and probable protein changes resulting from BVDV infection significantly alter cellular responses, and may have a profound impact on experimental outcome. Transcriptomic analysis provided the initial clues leading to the characterization of this altered function.