Background/Aims: To estimate the amount and nature of pupil centroid shift and cyclotorsion occurring between preoperative wavefront measurement and refractive surgery. Methods: This retrospective study comprised 183 eyes of 92 patients who had wavefront-guided LASIK using iris registration. We analyzed the pupil centroid shift and cyclotorsional displacement occurring between preoperative wavefront measurements and during the laser procedure. The eyes were measured by the WaveScan® Wavefront® system (VISX, Santa Clara, Calif., USA) and refractive surgery was performed with the VISX STAR S4 excimer laser system. Results: The mean magnitude of shifts in the location of pupil center was 0.26 ± 0.16 mm horizontally, 0.20 ± 0.16 mm vertically and 0.37 ± 0.13 mm vectorally. 162 eyes (88.5%) experienced more than 0.2 mm of shift. The mean amount of torsion was 2.58 ± 1.56° for 83 eyes showing incyclotorsion and 2.94 ± 1.87° for 100 eyes showing excyclotorsion. 117 eyes (63.9%) experienced more than 2° of cyclotorsion and 21 eyes (11.5%) experienced more than 5° of cyclotorsion. Conclusions: Pupil centroid shift and cyclotorsion occur in the majority of eyes undergoing laser treatment. The amount of pupil centroid shift and cyclotorsion shown in this study is considerable. Accurate compensation for cyclotorsion and pupil centroid shift may maximize the potential of visual quality of customized ablations.