A key to effective teaching is an awareness and accurate understanding of the thinking and implicit assumptions that students bring to the subject to be learned. In the absence of extensive Socratic interactions with students, one strategy to assess student thinking involves the use of concept inventories (CIs). CIs are typically multiple-choice assessments, constructed based on research into student thinking and language, and designed to reveal the presence of common misconceptions and implicit assumptions pertaining to a particular facet of a subject. Here we describe the open-source Biological Concepts Instrument (BCI), a diagnostic, multiple-choice instrument designed to provide instructors with a preliminary map of a number of basic ideas in molecular level biology. We describe the strategy behind its design, the research upon which it is based, item construction, and its possible uses as a means to reveal and address persistent and often unrecognized conceptual obstacles.