This prospective study assessed corneal flap morphology in 115 patients undergoing laser-assisted in situ keratomileusis (LASIK). Flaps were created using the Moria M2 90-μm or KM-5000D 110-μm microkeratomes. Flap thickness was measured using anterior segment optical coherence tomography at seven points in a 7-mm diameter zone 1 h, 1 day, 3 days, 1 week and 1 month after surgery. Flap accuracy, reproducibility, uniformity and changes over time were evaluated. The Moria M2 microkeratome created flaps with less accuracy in the centre than the KM-5000D microkeratome (114.06 ± 6.46 μm vs 128.39 ± 6.79 μm, respectively, at 1 week). For both microkeratomes, flap thickness varied between most of the peripheral areas and the central point. Both microkeratomes created flaps with good central predictability and reproducibility, but high variation and significant deviation from intended thickness were observed in peripheral flap thickness.