AIM: To compare the effect of suction on the macular thickness and retinal nerve fiber layer (RNFL) thickness during laser in situ keratomileusis (LASIK) used Ziemer FEMTO LDV femtosecond laser (Ziemer group) and Mona M2 automated microkeratome (Moria group) for flap creation. METHODS: Fourier -domain optical coherence tomography (FD -OCT) was used to measure macular thickness, ganglion cell complex thickness and RNFL thickness of 204 eyes of 102 patients with the Ziemer femtosecond laser (102 eyes) and the Mona M2 microkeratome (102 eyes) before surgery and 30min; 1, 3d; 1wk; 1, 3mo; 1y after surgery. RESULTS: The average foveal thickness and parafoveal retinal thickness 30min after the surgery were statistically more than that before surgery (Ziemer P<0.001, P=0.003 and Mona P=0.001, R=0.006) and the effect was less in the Ziemer group than that in the Moria group (P all <0.05). The ganglion cell complex thickness was not significantly changed in both groups (P all >0.05). The RNFL thickness was statistically less 30min after surgery in both groups (P=0.014, P<0.001), but the influence was less in Ziemer group than that in Moria group (P=0.038). However, the RNFL thickness had recovered to the preoperative level only 1d after surgery. CONCLUSION: The suction of femtosecond laser and mechanical microkeratome led to the increase in macular central fovea thickness and the decrease in RNFL thickness values at the early stage after LASIK. The effect of suction on macular and the RNFL thicknesses in Ziemer group is smaller than that in Moria group.