A semiautomatic image analysis method has been developed to characterize the morphology of the dimorphic yeast Kluyveromyces marxianus var. marxianus (formerly fragilis) NRRLy2415 undergoing alcoholic fermentation of cheese whey permeate. The method is capable of separating cells into six defined categories, varying from simple ovoid yeast cells to branched mycelial cells. A sample size of 300 cells was found to be sufficient to obtain a statistically significant categorization. The processing time for a sample was found to be approximately 90 min. In addition to qualitative characterization, the method permits the measurement of geometric properties such as the width, length, and volume of individual cells or clusters of cells. When the cells analyzed by the automatic method were categorized on a manual basis, the error level in the automatic routine was found to be less than 3%.