Cryogenic-temperature transmission electron microscopy (cryo-TEM) was fine-tuned to make it applicable to the study of a natural oil-based system. While liquid ethane, the cryogen of choice for specimen preparation, was found to dissolve the oil, we observed that the triglycerides found in many natural oils serve as cryoprotectants that allow vitrification of such oil systems in liquid nitrogen, a cryogen that provides relatively low cooling rates. Using the modified technique combined with digital imaging by a cooled CCD camera, we were able to directly visualize inverse micellar and liquid-crystalline aggregates formed in the soybean oil/soybean phospholipids/water/hexane system, which is commercially important in soybean oil processing. The method developed here should be widely applicable to other organic solvent-based systems.