The application of functional genomics toward the investigation of complex medical conditions has moved from a futuristic dream to a medical reality in less then a decade. The ability to examine the expression level of thousands of genes simultaneously has opened the door for entirely new approaches toward experimental observation and discovery. The resulting data from these genomic studies is being collected at an unprecedented scale. This wealth of data can present its own obstacles in terms of analysis. However, as new and more powerful means of examining these experiments are developed, medical science is reaping significant benefit. The power of microarray gene expression analysis has been directed at a diverse and complex array of diseases. As will be discussed in this article, the investigation of pulmonary hypertension has already benefited greatly from the application of this technology.