Billions of dollars are being invested by public and private agencies to study the human genome, with the ultimate goal of improving the diagnosis and treatment of human genetic disease. For monogenic disease, progress has been remarkable and for many of these, genetic discoveries have led to improved diagnosis, prevention and treatment. In contrast, for the much more common, complex diseases such as diabetes and cancer, progress has been far slower. Extensive media coverage caused naïve and unrealistically high expectations, which were followed by disappointment when dramatic results were not forthcoming rapidly. In fact, however, if one correctly assesses the complexity of the problem, progress has been exceptional. Using recently developed technology and huge genetic databases, rapid progress is expected in the coming decade. Even today, these studies are providing unique insights into the pathogenesis of complex disease, and these will undoubtedly be translated into additional tangible diagnostic or therapeutic tools in the coming years.