Purpose To evaluate the impact of myopic keratorefractive surgery on ocular alignment. Methods This prospective study included 194 eyes of 97 myopic patients undergoing laser refractive surgery. All patients received a complete ophthalmic examination with particular attention to ocular alignment before and 3 months after surgery. Results Patients with a mean age of 26.6 years and a mean refractive error of À 4.83 diopters (D) myopia were treated. Asymptomatic ocular misalignment was present preoperatively in 46 (47%) patients: a small-angle heterophoria (1-8 prism diopters, PD) in 36%; and a large-angle heterophoria (48 PD)/heterotropia in 11%. Postoperatively, the change in angles of 10 PD or greater occurred in 3% for distance and 6% for near fixation: in 7% of the patients with orthophoria, in 3% of those with a small-angle heterophoria, and in 18% of those with a large-angle heterophoria/heterotropia. No patient developed diplopia. The preoperative magnitude of myopia or postoperative refractive status was not related to the change in ocular alignment. The higher anisometropia was associated with a decrease in deviation (P ¼ 0.041 for distance and P ¼ 0.002 for near fixation), whereas the further near point of convergence tended to be related with an increase in near deviation (P ¼ 0.055). Conclusions Myopic refractive surgery may cause a change in ocular alignment, especially in cases with a large-angle heterophoria/heterotropia. There is also a chance of improvement of misalignment in patients with anisometropia.