Purpose: To identify the laser programming strategy that will achieve optimal refractive outcomes of LASIK with a topography-guided laser for eyes with a disparity between cylinder measured by manifest refraction and cylinder measured by topography. Setting: Six surgeons at 5 clinical sites in the USA. Design: Retrospective data review. Methods: Preoperative, treatment, and postoperative data on 52 eyes that underwent topographyguided LASIK with the WaveLight EX500 Contoura ® Vision excimer laser ablation profile in which the vectors representing the preoperative refractive cylinder and the cylinder measured by the WaveLight ® Topolyzer™ VARIO Diagnostic Device (Vario cylinder) differed by >/= 0.50D and/or >/= 10 degrees of orientation were analyzed retrospectively. Data were contributed by six surgeons using the laser at 5 different clinical sites. Vector analysis of postoperative cylindrical refractive error and the actual laser programming strategy was used to calculate the cylindrical correction that would, theoretically, have completely eliminated postoperative refractive cylinder. This was compared to expected results using the preoperative manifest cylinder, the topographic cylinder, and the Phorcides Analytic Engine (Phorcides LLC, North Oaks MN; Phorcides). For analysis, subjects were stratified on the basis of the vector difference between Manifest and Topo cylinder (High, >0.75 D; and Low, ≤0.75 D). Results: The poorest calculated theoretical outcomes were obtained with the manifest refraction (centroid: −0.43, 0.22; mean calculated error vector: 0.56 ± 0.42 D; p=ns). Better outcomes were obtained with the topographically measured refraction (centroid: 0.37, 0.02; mean calculated error vector: 0.47 ± 0.33 D; p=ns). The best outcomes were obtained with Phorcides (centroid: −0.15, 0.06; mean calculated error vector: 0.39 ± 0.28 D; p=ns). The mean error vector magnitude in the Phorcides Low group was significantly lower than for the Manifest and Topo Low groups (0.26 D vs 0.48 D and 0.33 D; p<0.01). The mean error magnitude in the Phorcides High group was nearly 0.25 D lower than for the Manifest High group (0.48 D vs 0.70 D; p<0.01), but was the same as for the Topo High group (0.48 D vs 0.48 D). Conclusion: Our study suggests that using the topographically measured cylinder or the cylinder selected by Phorcides will produce more desirable refractive outcomes than entry of the preoperative refractive cylinder as the basis for correction of myopia and myopic astigmatism with the WaveLight Contoura Vision excimer laser.