Tooth agenesis is characterised by the congenital absence of one or more teeth. The Pax9 gene has been associated with nonsyndromic forms.To investigate the molecular mechanisms, we evaluated specific haplotypes frequency in exon 3 of the Pax9 gene in 26 patients and 21 controls, using an Italian population.Presence of His239His and the Ala240Pro were confirmed in exon 3 of the Pax9 gene. A frequency of 20.2€ of the T allele at position 717 and a C frequency of 33€ of Ala240Pro polymorphism, that reached 40.5€ in the control group, were observed. The 39 C/C-240 C/C or G/Chaplotype which we defined Pax9hapl a had a proportion of 61.9€ in control individuals. The frequency of Pax9hapl a tested in the patients was different from controls, being 81.3€ in normalcy and 18.8€ in oligodontia (p<0.05).Our observations suggest that Pax9hapl a may have a protective effect against sporadic oligodontia.