The aim of this study was to evaluate morphological and functional malocclusion trait changes in 3- to 12-year-old children and to determine whether such functional traits at the 3, 4, and 5 years of age correlated with malocclusion severity score at 12 years of age. Two hundred and sixty-seven children (132 boys, 135 girls) were randomly selected for a follow-up study from a previous cohort of 560 subjects. Functional and morphological traits were clinically assessed. Five functional malocclusion traits: mouth breathing, atypical swallowing, thumb, pacifier sucking, and bottle feeding were assessed and evaluated. Intra-arch assessment involved measurements of incisor crowding, rotation of incisors, and axial inclination of the teeth. For inter-arch measurements, overbite, anterior open bite, overjet, reverse overjet, anterior crossbite, and buccal segment relationships were recorded. The weighted sum of recorded occlusal traits thus represented the total malocclusion severity score. The median morphological malocclusion severity score was almost the same at 3 and 12 years of age, while functional malocclusion decreased. Sucking habits (finger- or dummy-sucking, bottle feeding) until 5 years of age were statistically significantly correlated with an atypical swallowing pattern from 6 to 9 years (Spearman r = 0.178, P = 0.017), which in turn was statistically significantly correlated with the morphological malocclusion severity score (Spearman r = 0.185, P = 0.042) at 12 years of age. At an early age, the morphological severity score is related to the stage of dental development, while at a later period, malocclusion severity score is also the result of incorrect orofacial functions at an early stage of dental development.