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Purpose: To verify whether there exists any difference in higher order aberrations after undergoing myopic LASIK(laser in situ keratomileusis) with conventional ablation and customized ablation in different eyes of the same patient. Methods:This was a prospective randomized study of 54 myopic eyes (27 patients) that underwent LASIK using the Nidek EC-5000 excimer laser system (Nidek, Gamagori, Japan). Topography-guided customized aspheric treatment zone (CATz) was used in the first eye of the patient (study group) and the other eye of the same patient was operated on with conventional ablation (control group). Higher order aberrations [root-mean-square (RMS) in the 5-mm zone] of both groups were observed with the Nidek OPD-Scan aberrometer before and 3 months after LASIK. Preoperative mean refractive error was similar between two eyes of the same patient (t=-0.577, P＞0.05). Results: Preoperatively, higher order aberrations (RMS in the 5-mm zone) in the CATz ablation and conventional groups were (0.3600±0.0341) μm and (0.2680±0.1421) μm, respectively. This difference was not statistically significant (t=1.292, P＞0.05). Three months after LASIK, higher order aberrations (RMS in 5-mm zone) in the CATz ablation and conventional groups were (0.3627±0.1510) μm and (0.3991±0.1582) μm, respectively. No statistically significant difference was noted between pre- and postoperative higher order aberrations in the CATz group (t=-0.047, P＞0.05). However, a statistically significant increase in higher order aberrations was observed after conventional ablation (t=-5.261, P＜0.05). A statistically significant difference was noted in the increase of higher order aberrations after LASIK between groups (t=-2.050, P=0.045). Conclusion: LASIK with conventional ablation and topography-guided CATz ablation resulted in the same BSCVA (best spectacle-corrected visual acuity) 3 month after LASIK. Higher order aberrations were increased, but the increase of higher order aberrations after customized ablation treatment was less than that after conventional ablation.