Objective: To compare epithelial thickness measurements provided by optical coherence tomography with intra-operative epithelial breakthrough point, determined by the surgeon, to provide customized ablation depth upon transepithelial-phototherapeutic keratectomy (t-PTK) prior to corneal collagen crosslinking (CXL). Methods: Charts of 24 eyes (15 patients) were reviewed retrospectively. All patients were clinically diagnosed with keratoconus, and had undergone t-PTK followed by CXL. Epithelial thickness map was generated by Fourier-domain optical coherence tomography [RTVue, Optovue Inc., Fremont, CA, USA] pre-operatively, and the surgeon (GR) determined epithelial breakthrough point intra-operatively. Results: Average planned epithelial ablation depth was 53.1 ± 4.4um, 52.8 ± 5.9um, and 54.6 ± 4.6um for all eyes, eyes with central cones, and eyes with eccentric cones respectively. Average depth of epithelial breakthrough was 38.7 ± 8.5um, 43.8 ± 6.3um, and 34.5 ± 8.3um for all eyes, central cones, and eccentric cones respectively. The average minimum epithelial thickness measured by the OCT generated epithelial thickness map was 42.8 ± 6.8um, 44.9 ± 6.3um, and 41.2 ± 7.3um for all eyes, central cones, and eccentric cones respectively. There was NO statistically significant difference between average minimum epithelial thickness (44.9 ± 6.3 microns) and average epithelial breakthrough depth (43.8 ± 6.3 microns) in eyes with eccentric cones. Conclusions: results suggest that minimum epithelial thickness may be an effective marker in determining optimum epithelial ablation depth in eyes with eccentric cones. The results also indicate using epithelial thickness in the central zone of the OCT-generated map is an ineffective marker in planning epithelial ablation depth regardless of the location of the cone.