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Abstract Background Wavefront-optimized laser-assisted in situ keratomileusis (LASIK) ablation is the most commonly performed procedure in refractive surgery, but new technologies have become available. Our goal was to compare topography-guided (Contoura) and asphericity-guided (Custom-Q) customized ablation treatments for the correction of myopia with or without astigmatism. Methods This prospective, randomized, double-blind, contralateral eye study included 60 eyes of 30 patients with myopia or myopic astigmatism requiring femtosecond LASIK (FemtoLASIK) treatment. For each patient, one eye was randomized to undergo Contoura treatment, and the other underwent Custom-Q abaltion. Uncorrected distance visual acuity (UDVA), corrected distance visual acuity (CDVA), manifest refractive spherical equivalent (MRSE), sphere (SPH), cylinder (CYL), 6.0-mm total corneal aberration root mean square (RMS), coma (COMA), trefoil (TREF), and spherical aberration (SA) were measured and analysed after a 1-year follow-up. Results The UDVA was − 0.08 ± 0.06 logMAR in Contoura eyes and − 0.08 ± 0.05 logMAR in Custom-Q eyes (p = 0.309) after 12 months. Twenty-five eyes (83%) in the Contoura group and twenty-six eyes (87%) in the Custom-Q group had a UDVA of 20/16 at the end of 12 months, and 100% of eyes in both groups reached a UDVA of 20/25 or better. Ninety and 100% of eyes in the Contoura and Custom-Q groups, respectively, achieved a residual CYL ≤0.50 D (p = 0.237). No statistically significant difference was observed between the surgical techniques in the preoperative to 1-year postoperative changes for any of the parameters evaluated (MRSE, CYL, RMS, DEF, COMA, TREF, and SA). Conclusions The Contoura and Custom-Q techniques yielded excellent visual and refractive results, but the evidence did not reveal any clear differences between these two methods after 1 year of follow-up. Trial registration ReBEC - Registro Brasileiro de Ensaios Clínicos [Internet]: Rio de Janeiro (RJ): Instituto de Informação Científica e Tecnológica em Saúde (Brazil); 2010 -. Identifier RBR-8rs5kt Myopia and Astigmatism Topography-guided Refractive Surgery by Contoura Method Versus Customized by Asphericity in Contralateral Eyes: A prospective Double blind Randomized Study. Available from https://ensaiosclinicos.gov.br/rg/RBR-8rs5kt Date of registration: 02/03/2020 (dd/mm/yyyy). CAAE:96778718.9.0000.5192. Issuing authority: Plataforma Brasil. CEP:2.979.279. Issuing authority: HUOC.