Tooth agenesis is the congenital lack of permanent teeth, which is called oligodontia, when the number of missing teeth is 6 or more. Oligodontia affects more than 1 of 100 humans, but its pathogenesis is largely unknown. Tooth genesis depends on the complex interactions between environmental and genetic factors. The MSX1 gene, a member of homeobox gene family, encodes a DNA-binding protein, which is involved in many epithelial-mesenchymal interactions, leading to vertebrate organogenesis, and appears to be most critical during early tooth development. The MSH1 gene has 2 exons, separated by an intron, and its mutations, such as missense or frame-shift mutations, have been reported to be associated with tooth agenesis. In the present study, we sequenced the MSX1 gene of three unrelated patients with sporadic, non-syndromic oligodontia: 2 boys aged 8.5 and 15 years old and one girl aged 15.5 years old. We have thus identified a homozygotic deletion of 11 nucleotides in the intron, near the 5' splicing site, in two patients, who also carry a different exonic transition. The base changes we detected were not present in an open reading-frame of the MSX1 gene, but the newly identified deletion of 11 nucleotides might interfere with the splicing of the MSX1 gene. In contrast, the third patient, a 15-year boy, displayed no base change in the examined regions. Therefore, the identified 11-nucleotide deletion may decrease the expression level of the MSX1 protein, but the link with oligodontia needs further study.