The aim of this study was to evaluate facial morphology in 25 Class III and 46 non-Class III children aged 5-6 years using three-dimensional (3D) laser imaging; 3D facial images were obtained, two average facial templates were constructed for the non-Class III male and female groups, each individual face was superimposed on the corresponding average template and group comparisons were evaluated (facial height, facial convexity, mandibular position and facial surface morphology). Differences between parameters were evaluated by using an analysis of variance and colour deviation maps. The results showed that Class III children had less mid-face prominence and a concave facial profile when compared to non-Class III children (P = 0.002 and P = 0.018). The position of the pg point in the z-axis just failed to reach statistical significance when comparing the two groups (P = 0.051). A vertical analysis showed no statistical significance between the groups, when evaluating middle (n-sn) and lower (sn-pg) facial height. Coincidence of the Class III faces to normal templates with a tolerance set as 0.5 mm was low (less than 30%). The soft tissue characteristics of a Class III face differ significantly from the non-Class III face in the mid-face region and in the facial profile. A 3D laser imaging method evaluated and identified morphological characteristics of Class III children in deciduous dentition, which could in the future become an important diagnostic tool in small children. The most important clinical advantage of this study is the non-invasiveness of the method.