Objective To explore gene polymorphisms of 5,10-methylenetetrahydrofolate reductase (MTHFR) and 5-methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR) in women from Chinese Han population in Yantai city. Methods A total of 2 670 Han women were recruited in the study. Their oral epithelial cells were collected, followed by the extraction of genome DNA, in order to detect gene polymorphisms of MTHFR and MTRR using fluorescence quantitative PCR method. The Results were compared with those in other cities of China. Results The frequency of MTHFR 677CC, 677CT and 677TT of Han women in Yantai city were 18.6%, 49.2% and 32.2%, respectively. The frequency of MTHFR 677TT among women in Yantai city was obviously different from Weifang, Zibo, Zhengzhou, Zhenjiang, Wuhan, Deyang, Kunming, Guangzhou and Qionghai (P<0.05). The frequency of MTHFR 1298AA, 1298AC and 1298CC of Han women in Yantai city were 72.5%, 25.7% and 1.8%, respectively.The frequency of MTHFR 1298CC in Yantai was different from Weifang, Zibo, Linyi, Zhenjiang, Wuhan, Deyang, Kunming, Guangzhou and Qionghai (P<0.05). The frequency of MTRR 66AA, 66AG and 66GG of Han women in Yantai city were 54.6%, 38.1% and 7.2%, respectively. The frequency of MTRR 66GG in Yantai was only different from Zibo, Linyi and Qionghai(P<0.05). Conclusion The MTHFR, MTRR polymorphism distribution of Han women in Yantai city is different from other regions, showing region-specific characters.