A new undergraduate program in chemical biology was launched in 2008 to provide a unique learning experience for those students interested in this interdisciplinary science. An innovative undergraduate chemical biology laboratory course at the third-year level was developed as a key component of the curriculum. The laboratory course introduces students to some of the fundamental aspects of chemical biology through a series of integrated, research-based laboratory experiments, which illustrate how different areas of the discipline are interconnected. The 12-week stand-alone laboratory course consists of a weekly 1-h lecture and a 4-h laboratory period. During the course, students synthesize a novel anthraquinone natural product-like compound, purify a protein, and perform both an in vitro and an in vivo biological assay to investigate protein-ligand interactions with these materials. Two iterations of the course have been completed with class sizes of 21 (2010) and 11 (2011) students. Because of the modular nature of the course (i.e., organic, biological, and analytical sections), it is widely applicable to a range of upper-level chemistry, biology, molecular biology, and biochemistry undergraduate courses.