Corneal lamellar refractive surgery for myopia reduces the risk of corneal haze but adds to the risk of flap complications. We retrospectively determined the incidence of flap complications in the initial series of eyes undergoing lamellar refractive surgery by one surgeon. We assessed the incidence of flap complications overall, the trend in these complications during the surgeon's learning curve, and the impact of the complications on best spectacle-corrected visual acuity. Charts of the first 1,019 eyes that underwent myopic keratomileusis in situ or laser in situ keratomileusis were reviewed for flap complications and visual outcome. Of the 1,019 eyes, 490 eyes underwent myopic keratomileusis in situ, and 529 eyes underwent laser in situ keratomileusis. Eighty-eight (8.6%) of 1,019 eyes had flap-related complications. Six eyes had two complications. Intraoperative complications included irregular keratectomy in nine eyes (0.9%), incomplete keratectomy in three eyes (0.3%), and a free cap in 10 eyes (1.0%). The incidence of intraoperative complications was six (6.0%) in the first 100 consecutive eyes, 14 (2.3%) in the next 600 consecutive eyes (P = .04, chi-square test), and one (0.3%) in the last 300 eyes (P = .03, chi-square test). Postoperative complications included displaced flaps that required repositioning in 20 eyes (2.0%), folds in the flap that required repositioning in 11 eyes (1.1%), diffuse lamellar keratitis in 18 eyes (1.8%), infectious keratitis in one eye (0.1%), and epithelial ingrowth that required removal in 22 eyes (2.2%). The incidence of flap displacement and folds in 200 eyes in which we irrigated under the flap and allowed it to settle without further manipulation averaged 8.5%, whereas the incidence in other groups of 100 consecutive eyes averaged 0.8% (P < .00001, chi-square test). The incidence of diffuse lamellar keratitis was 0.2% in eyes that had undergone myopic keratomileusis in situ and 3.2% in eyes treated by laser in situ keratomileusis (P = .0003, chi-square test). No eye lost 2 or more lines of best spectacle-corrected visual acuity because of flap complications. Flap complications after lamellar refractive surgery are relatively common but rarely lead to a permanent decrease in visual acuity. Physician experience with the microkeratome and with the handling of the corneal flap decreases the incidence of flap complications.