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Aim The aim of the present study was to compare the differences in visual outcomes, higher-order aberrations and corneal asphericity, as measured by Q values, in patients undergoing laser in-situ keratomileusis using wavefront-guided variable-spot size VISX CustomVue and wavefront-optimized small-spot size WaveLight Allegretto platforms. Type of study This study was designed as a randomized, prospective, single-blinded, double-armed, fellow-eye comparative study. Patients and methods A total of 100 eyes of 50 patients undergoing customized laser in-situ keratomileusis for compound myopic astigmatism were enrolled and randomly divided into two groups. Each patient underwent full ophthalmological examination; aberrometry was performed on either eye by using VISX CustomVue aberrometer and Allegretto WaveLight aberrometer. Each patient had one eye examined using the Allegretto Wave eye Q system (small-spot scanning), and the fellow eye by using VISX Star CustomVue S4 system (variable-spot scanning). All patients were given postoperative steroids, antibiotic drops and artificial tears. First day postoperative visit was scheduled to check for flap stability, and to exclude complications. Clinical examination and best corrected visual acuity, corneal imaging and aberrometry were scheduled at 1 month and 1 year later. Results Final best corrected visual acuity showed insignificant difference between the two groups ( P = 0.712). The final differences between the groups were insignificant in all other parameters. Conclusion The two ablation profiles are highly comparable in treating compound myopic astigmatism.