To identify the potential factors affect that affect the thickness of corneal flaps created using 2 different microkeratome heads. Care-Vision Laser Centers, Tel-Aviv, Israel. Retrospective comparative study. The study included eyes in which bilateral laser in situ keratomileusis (LASIK) was performed from January 1, 2005, to December 31, 2012, using an SBK-90 microkeratome head (Group 1) or an M2-90 microkeratome head (Group 2). Inclusion criteria were at least 18 years of age, a stable refraction for 12 months, an intraocular pressure of less than 21 mm Hg, and no history of autoimmune disease, diabetes, ocular surgery, or eye disease. In addition, patients had to cease wearing contact lenses for 2 weeks (rigid lenses) or 4 days (soft lenses) before the preoperative evaluation and before surgery. The disposable blade was used in the right eye first and then reused in the left eye. The study evaluated 6242 eyes of 3121 patients with a mean age of 32.2 years ± 9.8 (SD). Group 1 comprised 2560 eyes (41%), and Group 2 comprised 3682 eyes (59%). The eyes in Group 1 had thinner flaps (P < .001). The right eyes had thicker flaps (P < .001). Flap thickness had a positive correlation with precutting central corneal thickness (CCT) and operating room humidity and a negative correlation with patient age, preoperative sphere and cylinder, and operating room temperature. Statistically significant differences were found in flap thickness between surgeons (P < .001). Larger suction rings created thicker flaps (P < .001). Stepwise regression models accounted for up to 28.1% of the variation in flap thickness. Factors that were significantly correlated with flap thickness included the precutting CCT, whether the right or the left eye, the microkeratome head used, the surgeon performing the procedure, and the preoperative sphere. These findings might help prevent post-LASIK corneal ectasia. No author has a financial or proprietary interest in any material or method mentioned.