Familial non-syndromic hypodontia shows a wide phenotypic heterogeneity and inherits in an autosomal-dominant, autosomal-recessive or X-linked mode. Mutations in genes PAX9, MSX1 and AXIN2 have been determined to be associated with autosomal-dominant tooth agenesis. Recent studies in two families showed that X-linked non-syndromic hypodontia resulted from EDA mutations. In this study, a novel EDA mutation (Thr338Met) that results in X-linked non-syndromic hypodontia in a Chinese family was identified. The patterns of tooth agenesis in these related subjects with defined EDA mutation were analyzed using comparative statistical analysis of tooth agenesis in EDA, MSX1 and PAX9. Statistically significant differences (p<0.001) were observed at eight positions. The resulting data of congenital absence of maxillary and mandibular central incisors, lateral incisors and canines, with the high possibility of persistence of maxillary and mandibular first permanent molars, appears as a pattern of tooth agenesis, suggesting the presence of an EDA mutation.