Introduction: Refractive surgery procedures, transepithelial photorefractive keratectomy (T-PRK) and femtosecond laser in situ keratomileusis (Fs-LASIK) are regarded as safe and efficacious methods for correcting myopia and myopic astigmatism. These two methods do not have much differences in results when treating spherical myopia, while some differences does exist in treatment of myopic astigmatism. Vector analysis presents powerful tool to show the real differences between these two methods regarding higher order ocular aberrations and central corneal thickness of treated eyes. Aim: The aim of the study is to investigate changes in higher order ocular aberrations (HOAs) and central corneal thickness (CCT) following treatment of myopia and myopic astigmatism above -5.00DS and up to -2.00DC after either T-PRK or Fs-LASIK. Methods: Patients (30 eyes per group) underwent T-PRK (group I) or Fs-LASIK (group II) procedure using Schwind Amaris 750S laser. HOAs (3mm&5mm pupil) and CCT were measured objectively at pre-, 1,3 & 6 months postop in each case. Results: Key results at 6 months were: i) mean values of trefoil (5mm pupil) were 0.092μm (sd,0.055,95% CI 0.072 to 0.112) & 0.126μm (sd,0.078,95% CI 0.098 to 0.154) in group I, and 0.088μm (sd,0.058,95% CI 0.067 to 0.109) & 0.064μm (sd,0.034,95% CI 0.052 to 0.076) in group II (P=0.001 at 6 months); ii) Changes in CCT (ΔCCT) and best spherical equivalent correction (ΔBSE) was significant in group II (ΔCCT=-26.55[ΔBSE]-14.06,R=0.486,P=0.006) but not in group I (p=0.034). Conclusions: After T-PRK trefoil is worse than Fs-LASIK. The predictability of corneal changes is better following Fs-LASIK.