Purpose:To compare outcomes in wavefront-guided LASIK performed with iris recognition software versus without iris recognition software in different eyes of the same patient. Methods: A randomised, prospective study of 104 myopic eyes of 52 patients undergoing LASIK surgery with the MEL80 excimer laser system was performed. Iris recognition software was used in one eye of each patient (study group) and not used in the other eye (control group). Higher order aberrations (HOAs), contrast sensitivity, uncorrected vision (UCV), visual acuity (VA) and corneal topography were measured and recorded pre-operatively and at one month and three months post-operatively for each eye. Results: The mean post-operative sphere and cylinder between groups was similar, however the post-operative angles of error (AE) by refraction were significantly smaller in the study group compared to the control group both in arithmetic and absolute means (p = 0.03, p = 0.01). The mean logMAR UCV was significantly better in the study group than in the control group at one month (p = 0.01). The mean logMAR VA was significantly better in the study group than in control group at both one and three months (p = 0.01, p = 0.03). In addition, mean trefoil, total third-order aberration, total fourth-order aberration and the total scotopic root-mean-square (RMS) HOAs were significantly less in the study group than those in the control group at the third (p = 0.01, p = 0.05, p = 0.04, p = 0.02). By three months, the contrast sensitivity had recovered in both groups but the study group performed better at 2.6, 4.2 and 6.6 cpd (cycles per degree) than the control group (p = 0.01, p < 0.01, p = 0.01). Conclusions: LASIK performed with iris recognition results in better VA, lower mean higher-order aberrations, lower refractive post-operative angles of error and better contrast sensitivity at three months post-operatively than LASIK performed without iris recognition.