OBJECTIVES: A novel, 3D technique to measure the differences in tooth crown morphology between the MSX1 cases and non-affected controls was designed to get a better understanding of dental phenotype-genotype associations. MATERIALS AND METHODS: Eight Dutch subjects from a single family with tooth agenesis, all with an established nonsense mutation c.332 C > A, p. Ser 111 Stop in exon 1 of MSX1, were compared with unaffected controls regarding several aspects of tooth crown morphology of incisor and molar teeth. A novel method of quantitative three-dimensional analysis was used to detect differences. RESULTS: Statistically significant shape differences were observed for the maxillary incisor in the MSX1 family compared with the controls on the following parameters: surface area, buccolingual dimension, squareness, and crown volume (P ≤ 0.002). Molar crown shape was unaffected. CONCLUSIONS: A better understanding of dental phenotype-genotype associations may contribute to earlier diagnosis of some multiple-anomaly congenital syndromes involving dental anomalies. CLINICAL RELEVANCE: A "shape database" that includes associated gene mutations resulting from developmental syndromes may facilitate the genetic identification of hypodontia cases.