The aim of the present study was to investigate the histopathological changes and wound healing process of rabbit corneas following conventional laser in situ keratomileusis (LASIK) with and without the complication of flap macrostriae. The right eyes of 14 rabbits underwent LASIK with the formation of flap striae (macrostriae group) and the left underwent LASIK alone (control group). Two rabbits were selected at random for sacrifice on days 1, 3, 7 and 14, and at 1, 3 and 6 months postoperatively. The histopathological characters of the corneas were compared by hematoxylin and eosin (H&E), periodic acid-Schiff (PAS) and Masson staining. In the control group, the epithelial basement membrane of the cornea exhibited microstriae and the arrangement of stromal collagen fibers was regular. The width of the microstriae in the flap was 20-40 µm one week after surgery and the microstriae were no longer visible two weeks postoperatively. In the macrostriae group, infiltration of polymorphonuclear cells occurred around the incision and irregular hyperplasia of the epithelium was observed due to undulation of the epithelial basement membrane on the first postoperative day. The collagen fibers and striae of the corneal stroma exhibited irregular undulation one month postoperatively. The area between the corneal flap and stromal bed was distinctly stained by PAS and Masson stains. Macrostriae with a width of 80-120 µm affecting two-thirds of the entire cornea remained visible six months postoperatively. In conclusion, the inflammatory reactions and clinical impact of flap macrostriae were severe. Macrostriae involving two-thirds of the entire cornea remained visible six months postoperatively. Longer-term studies are required to further elucidate the issues associated with corneal flap striae.