AIM: To assess peripapillary retinal nerve fiber layer (RNFL) and choroidal thickness obtained with enhanced depth imaging (EDI) mode compared with those obtained without EDI mode using Heidelberg Spectralis optical coherence tomography (OCT). METHODS: Fifty eyes of 25 normal healthy subjects and 32 eyes of 20 patients with different eye diseases were included in the study. All subjects underwent 3.4 mm diameter peripapillary circular OCT scan centered on the optic disc using both the conventional and the EDI OCT protocols. The visualization of RNFL and choroidoscleral junction was assessed using an ordinal scoring scale. The paired t-test, intraclass correlation coefficient (ICC), 95% limits of agreement (LoA), and Bland and Altman plots were used to test the agreement of measurements. RESULTS: The visibility score of RNFL obtained with and without EDI was of no significant difference (P=0.532), the visualization of choroidoscleral junction was better using EDI protocol than conventional protocol (P<0.001). Peripapillary RNFL thickness obtained with EDI was slightly thicker than that obtained without EDI (103.25±9.42 μm vs 101.87±8.78 μm, P=0.010). The ICC of the two protocols was excellent with the value of 0.867 to 0.924, the 95% LoA of global RNFL thickness was between -10.0 to 7.4 μm. Peripapillary choroidal thickness obtained with EDI was slightly thinner than that obtained without EDI (147.23±51.04 μm vs 150.90±51.84 μm, P<0.001). The ICC was also excellent with the value of 0.960 to 0.987, the 95% LoA of global choroidal thickness was between -12.5 to 19.8 μm. CONCLUSION: Peripapillary circular OCT scan with or without EDI mode shows comparable results in the measurement of peripapillary RNFL and choroidal thickness.