Both fresh frozen brain tissue and formalin-fixed paraffin-embedded (FFPE) human brain tissue are invaluable resources for molecular genetic studies of diseases of the human nervous system, especially neurodegenerative disorders. To identify the optimal method for DNA extraction from human brain tissue, we compared several DNA extraction methods on differently processed tissue. Fragments of LRRK2 gene were amplified for evaluation. Results: DNA was successfully extracted in 100% of the fresh frozen tissue samples using either a commercial kit (QIAamp DNA Micro) or a laboratory-based method (boiling the samples in 0.1M NaOH, followed by proteinase K digestion, and then DNA extraction using Chelex-100). However, larger quantities of genomic DNA were extracted using the laboratory-based method in comparison to the commercial kit. In the case of FFPE tissue samples, the success rate for DNA extraction was greater when using the commercial kit compared to the laboratory-based method (DNA extracted from 76% versus 33% of tissue samples). Conclusion: although the present results demonstrate that PCR-amplifiable genomic DNA can be extracted from both fresh frozen and FFPE human brain tissue samples, obtaining fresh brain tissue is recommended for DNA extraction in future neuropathological studies, and for a maximal yield of geneomic DNA laboratory-based methods are recommended.