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Tooth development (odontogenesis) is a very complicated and complex process involving interplay between oral epithelium and adjacent ectomesenchyme. These reciprocal interactions are mediated by more than 300 signaling molecules (e.g. PAX9, AXIN2 and MSX1). Mutations in the genes for these two regulation proteins were associated with isolated (non-syndromic) form of hypodontia and for this reason; we decided to study gene mutations for MSX1 gene. Upon receipt of approval from the Ethical Commission of University Hospital Ostrava (No. 638/2011), DNA was isolated from patients using Ultra Clean Blood Spin DNA Isolation Kit (Mo-Bio). Blood samples or buccal swabs from 200 Czech patients with various types of tooth agenesis were used for this purpose. PCR products for exons of MSX1 gene were prepared using Kapa 2G Robust Hot Start polymerase (KapaBio Systems) and sequenced using ABI 3130 Prism (Life Technologies) genetic analyzer. Finally, sequences were compared to standard sequences of the genes and mutations were described according to their possible effect to the protein structure. We identified novel heterozygous MSX1 gene polymorphism that may cause amino acid substitutions Ala40Gly. This mutation was found both in the group of patients suffering from hypodontia and in the control group. Furthermore, intron and exon mutations without influence on amino acid change have been identified. These changes in nucleotide sequence have no direct effect on protein structure; however they can affect stability and regulation of gene expression. Therefore, detailed analysis of the results and the future research has to be focused on familiar studies and relationship between mutations in MSX1 gene and tooth agenesis (hypodontia, oligodontia) as well as on analysis of other genes coding proteins participating in odontogenesis, such as PAX9 or AXIN2. The project was supported by the IGA MZ CR, project no. NT 114206 6/2010.