Measurement of sublayer thickness and transparency at cellular level in the living animal are critical to understanding the role of specific transgenes and transgene products in controlling corneal development and maintenance of transparency. Using two different transgenic mouse strains having altered corneal clarity, we have evaluated the ability of in vivo confocal microscopy to measure corneal haze and localize light scattering structures. Projection of 2-D and 3-D image information identified the nature and location of light scattering within the cornea and allowed correlation of unique structural differences to transgene expression. Our findings suggest that in vivo confocal microscopy can be used to identify the effects of transgene expression on mouse corneal transparency.