Treatment of samples of digested endosperm with SDS resulted in a homogenous suspension of single starch granules that was suitable for analysis by flow cytometry without altering their refractive properties. Flow cytometry can be used for more rapid and accurate enumeration of starch granules than can be achieved with a hemocytometer as with the latter the number of starch granules seems to be underestimated. Moreover, flow cytometric analysis based on forward angle light scatter (FALS) and absorbance properties revealed that there are at least three unique subclasses of starch granules that appear during kernel development. The first subclass contained mainly small granules (2–5 μm) whereas the second subclass generally consisted of large granules (> 5 μm). However, within a given size, there were two distinct subpopulations with significantly different absorbance properties. The physiological or physicochemical significants of these subclasses warrant further investigation.