Fourier transform methods were applied to STEM (scanning transmission electron microscopy) images to detect and quantify the subtle differences between the structure of normal transparent calf cornea and opaque calf cornea. In order for a tissue to be transparent, it can scatter or absorb only a small amount of light. Light scattering is minimized when the principal Fourier components of the spatial fluctuations in the index of refraction have wavelengths which are small relative to the wavelength of light (Benedek, 1971). Corneal opacity was produced as a result of high intraocular pressure (100-150 mmHg) when liquid was injected into calf eyes (0-2 weeks old). Pressurization created large structural defects and slight disruptions in the organization of the collagen fibers. Although the fiber organization appeared similar in the micrographs of both opaque and transparent corneas, Fourier analysis of STEM images collected at 50K magnification identified statistically significant differences. Far fewer Fourier components with wavelengths in the light scattering range (200-1100 nm) were observed in the transparent corneas than in the pressurized corneas as predicted by Benedek's theory. It was of interest that corneas treated with 100% glycerol prior to pressurization remained transparent at high intraocular pressures, possibly because glycerol stabilized the structure of the corneas and maintained a uniform index of refraction across the corneal stroma. The results demonstrate the effectiveness of Fourier analysis in detection and quantification of slight changes in structure at the electron microscopic level.