An increasing number of evidence supports the assumption that genetic factors have crucial role in the development of periodontitis and hypodontia. The strategic purpose of the authors is to identify the genetic background of these disorders and to map the gene polymorphisms involved in their development. As a first step of an experimental series, we aimed to set and optimize multiple individual gene polymorphism identification methods by the combination of polymerase chain reaction and restriction fragment length polymorphism analysis methods. We have successfully optimized eight single nucleotide polymorphism procedures that are potentially involved in periodontitis (IL-1 alpha -889, IL-1 beta -511, IL-1 beta +3954, IL-6 -174, IL-10 -1082, TLR-4 -299, TLR-4 -399, TNF-alpha -308), and another two that might be related to the appearance of hypodontia (PAX9 -1032, PAX9 -912). Besides the dominant allele, we also observed the presence of the rare allele in each polymorphism although at present we have a small sample number. These preliminary studies provide evidence for the feasibility of further investigations with large sample numbers comparing control and patient groups. These studies may lead to the development of new diagnostic strategies and provide novel tools for the early recognition of genetic predisposition and the primary control of the diseases. Furthermore, they project future therapeutic avenues for gene therapy in the cure and prevention of oral disorders.