OBJECTIVE To observe the changes of pathology and ultra- microstructure of corneal lenticules extracted by femtosecond laser small incision lenticule extraction surgery and to investigate instantaneous damage of photodisruption of femtosecond laser to human corneal tissue in vivo. METHODS The small incision lenticule extraction surgeries in 25 myopic eyes were performed with Carl Zeiss VisuMax femtosecond laser, and the lenticules were observed by light microscopy, scanning electron microscopy and transmission electron microscopy. RESULTS Light microscopy showed slight edema in part of the collagen fibers in the cornea lenticule tissue. A thin layer of deep tissue dyeing at the edge of the lenticule was observed on a linear array. In the center of superficial lenticule tissue existed a few bubbles. Under the scanning electron microscope, the anterior surface of the lenticule was found to be relatively smooth, with no obvious tissue bridge. The posterior surface of the lenticule was slightly irregular compared with the anterior surface. Scattered tissue bridges and residual traces of the effect of femtosecond laser photodisruption could be observed. Under the transmission electron microscope, adjacent collagen fiber layers in the corneal lenticule matrix were detected to cross each other regularly, with no breakage of the collagen fibers or separation of the layers. The incision of the collagen fibers on one side of the lenticule was on a linear alinement. It can also be observed that the central part of the lenticule was mildly damaged. However, the stroma cells near the lenticule limbus were severely damaged. Part of the corneal stroma cells were solidified with several shivers, which might be due to the photodisruption. Some of the damaged corneal stroma cells were observed with remnants, while the spaces occupied by part of the corneal cells became fractured. CONCLUSIONS Obvious damage of the femtosecond laser to the corneal tissue at early stage was not observed. At the edge of the area where femtosecond laser focused, there were mild thermal injury and slight structure change. There were not abnormal appearances of the tissue structure at the non-focus area.