Background Thin-flap laser in situ keratomileusis (LASIK) is the new trend of refractive error correction surgery, the formation of corneal flap is crucial for a success of LASIK surgery. This study aimed to assess and compare the variations of LASIK flap created by the IntraLase femtosecond laser, Mona One Use-Plus SBK and Mode M2 Single-Use 90 mu m-head microkeratome using Anterior segment optical coherence tomography (Visante OCT). Methods One hundred and sixty-one eyes of 81 consecutive patients were enrolled in this prospective study and randomly divided into three groups depending on the flap creation method: flap creation with the the IntraLase femtosecond laser (IntraLase group, 59 eyes), flap creation with the Mona One Use-Plus SBK (SBK group, 44 eyes), and flap creation with the Mona M2 Single-Use 90 pm-head microkeratome (M2SU90 group, 58 eyes). The nominal flap thickness was 110 mu m for all patients and for the three devices. One month after surgery, Visante OCT was used to measure the flap thickness at 20 locations on each cornea and the results were assessed for uniformity, regularity, and accuracy. Results At 1 month after surgery, the mean central flap thickness was (111 +/- 3) mu m in the IntraLase group, (114 +/- 8) mu m in the SBK group, and (118 +/- 13) mu m in the M2SU90 group respectively. The flaps in the IntraLase group and the SBK group were more regular, showing an almost planar configuration, than the meniscus-shaped flaps in the M2SU90 group. The maximum deviation from the intended flap thickness (110 mu m) was 6 mu m in the IntraLase group, 10 mu m in the SBK group, and 20 mu m in the M2SU90 group respectively. A difference greater than 20 mu m was observed in 0.42% of measurements in the IntraLase group; 2.95% of the measurements in the SBK group and 21.12% of measurements in the M2SU90 group. Conclusions The flaps created by the IntraLase femtosecond laser and Mona One Use-Plus SBK are more uniform; more regular, and more accurate than those created by the Mona M2 Single-Use 90 mu m-head microkeratome. The first two methods can make precise flaps for Sub-Bowman Keratomileusis.