Objective To search for a genomic DNA extraction sample source characterized by rapid, effective, low cost, noninvasive, and suitable for large-scale epidemiological studies considering sample acquisition, storage and DNA extraction methods. Methods DNA samples were extracted and detected from blood cells with separating gel, ethylenediaminetetraacetic acid (EDTA) anticoagulant blood, coagulated blood cells after serum separation, fresh saliva, saliva stored at -20℃ for 1 month, saliva with 2 kinds of saliva protective solutions and oral mucosal epithelial cell samples obtained by cotton swab. The stability of genomic DNA obtained from different samples were verified. Two DNA samples with eligible quality control were randomly selected from one subject, and methylenetetrahydrofolate reductase (MTHFR) C677T gene polymorphism was genotyped using high-throughput sequencing. Results Separating gel seriously reduced the DNA extraction effect, and the qualified rate of DNA samples was 37.7% (1 130/3 000) in blood cells with separating gel. The DNA extraction efficiency from EDTA anticoagulant blood was good, with the DNA concentration being (180.20±20.30) mg/L and D₂₆₀/D₂₈₀ being 1.90±0.10. In coagulated blood cells after serum separation, remarkable DNA degradation was found, with the DNA concentration being 28.91-34.53 mg/L. The concentrations of DNA extracted from fresh saliva and saliva stored at -20℃ for 1 month were both qualified without significant difference (P>0.05). The concentrations of DNA extracted from saliva with 2 kinds of protective solutions were also qualified without significant difference (P>0.05). The concentration of DNA extracted from oral mucosal epithelial cells was (48.41±9.81) mg/L, which was lower than that from saliva samples. High-throughput sequencing showed that amplification of targeted gene fragments in vitro and genotyping detection of polymorphic sites of the MTHFR C677T gene could be achieved using the qualified DNA samples screened according to the quality control criteria. Conclusion Blood and saliva are eligible samples for extracting genomic DNA. Saliva has served as a better source sample to obtain human genomic DNA with low cost, no trauma and good quality.