Objective: Formalin fixed, paraffin-embedded (FFPE) archival tissues are valuable resources for many molecular studies. The goal of this study is identify the optimal method for DNA extraction from FFPE tissues. Method: 32 human gingival tissues which has obtained from patients with gingival hyperplasia were used. Serial sections of 10 μm thickness obtained using a standard microtome. Half of the sections were deparaffinized on glass, the other half collected directly to a 1,5 ml tube. In order to identify the optimal method for DNA extraction, we compared phenol-chloroform protocol and DNA Extraction Mini Kit. The duration of proteinase K digestion were also compared. Spectrophotometric evaluation of the yield and purity of DNA was conducted. To deteminate the amplifiablity of extracted DNA, three different bp fragment of the beta-globin gene were amplified using PCR. Results: The phenol-chloroform method had the lowest yield and purity. Deparaffinized specimens on glass, digested for 72 h and isolated using mini kit had the highest yield. Amplification of the 120 bp fragment of beta-globin gene was successful in all samples. Conclusion: According to our results deparaffinization on glass, increasing the time of proteinase K digestion and using commercial kits for isolation seems the best method to obtain amplifiable DNA from archival specimens.