An aqueous density fractionation for calcifying tissues was tested for its ability to prepare fractions corresponding to precise mineralization stages, suitable for further protein and crystal studies. Two fractions of immature enamel corresponding to different densities were prepared, using cooled cesium salt saturated solutions, and compared for crystal size and amelogenin molecular weight distribution. For the first time, a steep increase in crystal width was directly correlated to protein degradation in keeping with increasing mineralization. Thus, this paper describes a method for obtaining an accurate fractionation of a calcifying tissue according to its true density heterogeneity. The recovered fractions are shown to be suitable for both crystal and protein studies.