Recent developments in molecular biology have markedly speeded the processes involved in determining the molecular etiology of human Mendelian disorders. Nowhere are these changes more evident than in the field that is variously termed molecular dysmorphology, human morphogenesis, or human developmental biology. In contrast to the rapid changes in molecular genetics analysis, the processes and approaches of the clinical component of molecular dysmorphology have not changed substantially, and clinical analysis is therefore becoming relatively slower than molecular discovery. If clinical discovery is to maintain its deserved position at the forefront of human genetics research, new methods must be developed to acquire, archive, and analyze these data. The limitations of current phenotyping, specifically, the limitations of the collection and archiving of clinical data in medical journal case reports and case series manuscripts are demonstrated. Several provocative approaches that have been proposed to advance the field of clinical analysis are reviewed. Lastly, a specific proposal for a system of clinical analysis and archiving of data on human pleiotropic developmental anomaly syndromes is proposed to address these limitations.