To assess the corneal architecture and reproducibility of LASIK flap thickness created by the Amadeus II mechanical microkeratome (Ziemer Ophthalmic Systems AG) using Fourier-domain optical coherence tomography (OCT; Optovue Inc). Anterior segment Fourier-domain OCT was used to analyze the morphology of 58 LASIK flaps from 30 patients created with the Amadeus II microkeratome 140-μm head and ML7090CLB blades (Med-Logics Inc) at 2 weeks postoperatively. Flap thickness was assessed at 10 points across the central 6 mm of the cornea (horizontal and vertical meridians). Postoperative central corneal flap thickness measured by Fourier-domain OCT was compared with intraoperative ultrasound pachymetry measurements. No significant difference was noted between central flap thickness measured by intraoperative pachymetry (107.2 ± 14 μm) and postoperative OCT (111.7 ± 11 μm; P=.07, correlation coefficient=0.86). Fourier-domain OCT measurements demonstrated functionally planar flap architecture (standard deviation [SD] of thickness across the flap=4.9 μm, SD range across the flap=2 to 9 μm) for the microkeratome flaps. The Amadeus II microkeratome with Med-Logics blades created thin, reproducible, functionally planar flaps as measured by Fourier-domain OCT. Central flap thickness measured by intraoperative ultrasound pachymetry was equivalent to that measured 2 weeks postoperatively by OCT.