PURPOSE: To compare the changes in the histomorphology and immunofluorescence of collagen type I in clear corneal incisions (CCIs) at the end of bimanual and coaxial phacoemulsification in rabbits. SETTING: Iladevi Cataract and IOL Research Centre, Ahmedabad, India. METHODS: In this randomized study, the left eye of 30 rabbits had bimanual phacoemulsification through 1.2 mm CCIs for phaco tip access accompanied by an additional 1.4 mm incision for irrigating chopper access or coaxial phacoemulsification through a 2.6 mm single-plane CCI. The right eyes acted as controls. Samples collected at the end of surgery were processed for histomorphology using periodic acid-Schiff-hematoxylin staining and immunofluorescence localization of type I collagen. RESULTS: Incisions exposed to bimanual phacoemulsification had loss of epithelium, stromal fiber shrinkage, keratocyte nuclei fragmentation and condensation, ragged tunnel margins, and Descemet membrane and endothelial cell loss. The changes were minimal or absent in incisions exposed to coaxial phacoemulsification. Immunofluorescence showed a loss of parallel arrangement of type I collagen fibers in bimanual phacoemulsification incisions, while the fibers were well preserved in coaxial phacoemulsification incisions. The changes were more prominent in the roof of the incision tunnel than in the floor. CONCLUSIONS: Corneal incisions for bimanual phacoemulsification were more prone to damage than those for coaxial phacoemulsification. This may be attributed to the absence of a sleeve, which places the incision tunnel in direct contact with the metal phaco tip.