Stereology is a volume estimation method, typically applied to diagnostic imaging examinations in population studies where planimetry is too time-consuming (Chapman et al. Kidney Int 64:1035-1045, 2003), to obtain quantitative measurements (Nyengaard J Am Soc Nephrol 10:1100-1123, 1999, Michel and Cruz-Orive J Microsc 150:117-136, 1988) of certain structures or organs. However, true segmentation is required in order to perform advanced analysis of the tissues. This paper describes a novel method for segmentation of region(s) of interest using stereology data as prior information. The result is an efficient segmentation method for structures that cannot be easily segmented using other methods.