The integration of biomarkers reporting on drug pharmacodynamics or on a disease state is becoming necessary in the cost-effective design of clinical trials. Transcriptional changes in skin measured using whole-genome arrays have been useful in assessing the disease state in dermatology. Not only are skin biopsies well-tolerated and easy to obtain, but they sample a system in which many complex signaling and developmental networks are active and in which a wide variety of drug targets may be expected to play a role, either directly or indirectly. Recent advances have led to the use of transcriptional profiling of skin for making pharmacodynamic measurements in clinical trials, even for non-dermatological conditions.