PURPOSE: To compare the uniformity and accuracy of LASIK flaps created with a femtosecond laser versus a mechanical microkeratome using optical coherence tomography (OCT). METHODS: A prospective study was performed on 72 consecutive patients who underwent LASIK in both eyes in alternating fashion with either the AMO IntraLase FS60 (72 eyes) or the Moria M2 microkeratome (72 eyes). One month after surgery, anterior segment OCT was performed on each eye to measure flap thickness at 20 locations and the results were assessed for uniformity and accuracy. RESULTS: At 1 month after surgery, the microkeratome group flap ranges were greater than those found in the femtosecond laser group (P < .05). The meridian and radial flap uniformity in the femtosecond laser group were better, showing an almost planar configuration, than the meniscus-shaped flaps created with the microkeratome. Comparison of the nasal and temporal flap thickness revealed more regularity in the femtosecond laser group than the microkeratome group. The maximum deviation from the intended flap thicknesses was 7 mu m in the femtosecond laser group compared to 26 mu m in the microkeratome group. During the 1440 measurements of the 72 eyes, a difference similar to 20 mu m was observed in 0.42% of eyes in the femtosecond laser group and 15% of eyes in the microkeratome group. CONCLUSIONS: LASIK flaps made with the IntraLase FS60 were more uniform with more accurate thickness than those created by the Moria M2 microkeratome. [J Refract Surg. 2011;27(6):408-416.] doi:10.3928/1081597X-20101029-01