AIM:To define the microscopic cornea changes with in vivo laser scanning confocal microscopy after phacoemul-sification. METHODS: Thirty eyes were assigned to undergo cataract extraction by ultrasonic phacoemulsification in China Medical University. The morphologies of corneal layer by layer were evaluated in vivo with the Heidelberg Retina Tomograph III-Rostock Cornea Module (HRT-III RCM) confocal microscope pre- and post-operation for up to six months. RESULTS: For morphology, some irregular segments of nerve fiber were most pronounced seven days post-operation. Stroma keratocytes were obvious compared with the pre-operative condition. Corneal endothelial cells become obviously swollen in both the cytoplasm and nucleus. At six months, corneal cell and nerve morphology recovered to normal. CONCLUSION: Microstructural abnormalities were identified at each level of the cornea recovery process after phacoemulsification and lead to corneal morphology changes, but these could be recovered to normal in six months.