Structure-based drug design (SBDD) combines the power of many scientific disciplines, such as X-ray crystallography, nuclear magnetic resonance, medicinal chemistry, molecular modeling, biology, enzymology and biochemistry, in a functional paradigm of drug development. The current strength of SBDD lies in parlaying enzyme inhibitors into drugs, but a variety of technological advances over the past few years now makes it possible to address complex biological targets, such as those regulating immunosuppression and immunoactivation. Manual Navia and Debra Peattie discuss the SBDD paradigm and consider several of its achievements and challenges in immunopharmacology, particularly as these apply to the design of novel, potent immunosuppressants.