The effect of ultrasonic treatments (28, 45, and 100 kHz) as sterilization on Saccharomyces cerevisiae was investigated both by colony-forming ability and by a confocal laser-scanning microscope (CLSM), using a fluorescence staining approach with MDY-64 for endoplasmic reticula and Rhodamine B for mitochondria. The ultrasonic treatments, especially at the lower frequency of 28 kHz, were effective for sterilizing S cerevisiae, thus inducing the remarkable decrease in colony counts of S cerevisiae on YPD plate medium, but with some inactive (dead) cells. The CLSM images of fluorescence-stained organelles in the cell showed the intracellular fracture and the increase in fluorescent intensities of MDY-64 for endoplasmic reticula and Rhodamine B for mitochondria without cell membrane collapse by the ultrasonic treatments, especially at 28 kHz. The effect of the conditions (frequency, power, medium, and so on) of the ultrasonic treatments on cell components such as biological membranes would be different, thus inducing the effective and selective sterilization of some types of microorganisms.