Laser welding of corneal tissue is an alternative technique to conventional suturing procedures in ophthalmic surgery. The welding effect is achieved after staining the wound with a chromophore (Indocyanine Green, shortly: ICG) and then irradiating it with a low power diode laser. We present a study on the healing process of corneal wounds using Multispectral Imaging Autofluorescence Microscopy (MIAM). This technique is based on the characterization of fluorescence arising from tissue components (autofluorescence): it is particularly useful in studying corneal tissue, because it is mainly composed of type I collagen, one of the most important endogenous fluorophores. Laser welding tests of the cornea were carried out on rabbits in which full thickness corneal cuts of about 5 mm were sutured using a diode laser emitting at 810 nm, with a power of 80 mW. Bioptic sections of rabbit corneas were examined in a follow up study of 90 days after surgery, and the results were complementary to histological analysis performed in previous studies. Autofluorescence images showed a faster healing process and a better reorganization of the architecture of stromal fibers, in comparison with conventional suturing procedures. MIAM technique can represent a new tool to study the morphology of corneal tissue, offering some real advantages with respect to standard histological analysis. In fact, it does not require any chemical manipulation of the samples, providing information on the biological structure by directly monitoring distribution and emission intensity of endogenous fluorophores.