A novel approach is described using primary literature manuscripts for the final examination of an upper level undergraduate course in virology. This innovative technique was applied as an alternative to a core comprehensive final examination. A recent primary literature paper in virology was assigned several weeks before the end of the semester. Students were instructed to procure the electronic version of the manuscript, and to thoroughly read, highlight and outline the manuscript in advance. The examination was administered with an open book format and students were encouraged to bring laptops to access information as needed to answer questions. This primary literature-based examination format is presented here as an alternative to a comprehensive final exam. By comparing student examination scores for both final examination formats over a period of 11 years, it was determined that student performance was strong and not statistically different when compared to conventional comprehensive final examinations. Thus, the examination format described here was a useful assessment tool that provided students with valuable exposure to the discipline specific primary literature. While this article describes an application to an undergraduate virology course, the same examination techniques could be successfully applied to examinations in undergraduate or graduate classes in any areas of biochemistry and molecular biology.