Background Copernicus optical coherence tomography (SOOT) is a new, ultra high-speed and high-resolution instrument available for clinical evaluation of optic nerve. The purpose of the study was to compare the agreements between SOOT and Heidelberg retinal tomography (HRT). Methods A total of 44 healthy normal volunteers were recruited in this study. One eye in each subject was selected randomly. Agreement between SOOT and HRT-3 in measuring optic disc area was assessed using Bland-Altman plots. Relationships between measurements of optic nerve head parameter obtained by SOOT and HRT-3 were assessed by Pearson correlation. Results There was no significant difference in the average cup area (0.306 vs. 0.355 mm, P=0.766), cup volume (0.158 vs. 0.130 mm, P=0.106) and cup/disc ration (0.394 vs. 0.349 mm, P=0.576) measured by the two instruments. However, other optic disc parameters from SOOT were significantly lower compared with HRT-3. The Bland-Altman plot revealed good agreement of cup area and cup volume measured by SOOT and HRT-3. Bad agreement of disc area, rim area, rim volume and cup/disc ratio were found between SOOT and HRT-3. The highest correlations between the two instruments were observed for cup area (r(2)=0.783, P=0.000) and cup/disc ratio (r(2)=0.669, P=0.000), whereas the lowest correlation was observed for disc area (r(2)=0.100, P=0.037), rim area (r(2)=0.275, P=0.000), cup volume (r(2)=0.005, P=0.391) and rim volume (r(2)=0.021, P=0.346). Conclusions There were poor agreements between SOOT and HRT-3 for measurement of optic nerve parameters except cup area and cup volume. Measurement results of the two instruments are not interchangeable. Chin Med J 2012;125(16):2858-2861