The development of the prostate is an emerging priority area for prostate biologists. Early changes in prostate development permanently alter prostate morphology and function and an understanding of the permanent nature of early events that may influence the onset of late-life disease is vital. Two of the inherent problems involve associating exposure in early life with outcome in late life or maturity and accounting for the influence of genetic, environmental, dietary or metabolic factors during the intervening period. Any one of these factors, alone or in combination, might lead to an explanation of the discrepancies found in the literature regarding the influence of early changes to the prostate in later life. Therefore, it is important to establish a causal link between the hormonal changes that occur during the fetal/neonatal period and that imprint the gland and the onset of late-life pathology. In order to achieve this goal, several technical challenges need to be overcome to permit the objective assessment of prostate branching morphogenesis. Stereological techniques now allow the quantification of several parameters of branching morphogenesis and the identification of specific early changes that are permanent and irreversible with a late-life outcome. This methodology provides the means to determine the action of a range of genes or hormone/growth factors that have been implicated in prostate development and disease.