The purpose of this study was to assess the accuracy of two web-based automated cephalometric landmark identification and analysis programs. Manual landmark identification using Dolphin Imaging software was used as reference. 105 cephalograms were selected and divided into three groups of 35 subjects each, Class I, II and III. Radiographs were traced using Dolphin imaging software. WebCeph™ (South Korea) and Cephio™ (Poland) were used for the automated cephalometric analysis. Bland-Altman limits of agreement and the concordance correlation coefficient (CCC) were calculated. Kruskal Wallis test was used to compare the accuracy of WebCeph™ and Cephio™ measurements between the three groups. Mann-Whitney U test was used to compare the absolute difference between cephalometric measurements obtained using WebCeph™ and Cephio™. The mean difference (MD) between AI and manually-derived measurements was less than 1mm/degree and ranged from 0.01 to 0.8 except for upper lip protrusion (MD 1.35°), nasolabial angle (MD 5.01°), SN-GoGn (MD 1.41°), Ramus height (MD 1.46°), and IMPA (MD 1.94°). The mean CCC was 0.91 (range 0.60 to 0.96). No statistically significant differences were found between the three malocclusion groups for most of the measurements (P > 0.05). For most of the measurements, automated cephalometric measurements were clinically acceptable. Few differences were found between Webceph™ and Cephio™ for most measurements. Measurements including SNA, SN-PP, IMPA as well as soft tissue measurements require extra consideration and manual adjustment of respective landmarks for higher precision and improved efficiency.