Cornea functions as an outermost lens and plays an important role in vision. For cornea diagnosis and treatment, a microscopic imaging system with cellular resolution and high eye safety is strongly desired. Recently, the cell morphology of corneal epithelium and endothelium can be revealed by confocal or two-photon fluorescence microscopy, while the collagen fibers in the corneal stroma can be shown by second harmonic generation (SHG) microscopy. However, in most of the developed imaging tools, visible to near-infrared light sources were used. To increase the eye safety, a light source with longer wavelength would be needed. In this presentation, a study using an infrared laser based nonlinear microscopy to investigate the ocular tissues of a mouse eye will be demonstrated. Since most of autofluorescence was suppressed under infrared excitation, third harmonic generation (THG) microscopy was used to revea the cellular morphology and ~700?m penetrability could be achieved. Combining SHG with THG, in an intact mouse eye, not only the cornea but also the upper half of the lens could be observed with cellular resolution. Our study indicated that infrared-based SHG and THG microscopy could provide a useful in vivo investigating tool for ophthalmology. © 2009 SPIE.