Objective To study the relationship between the polymorphism of estrogen receptor ? gene (ER?)and unknown aetiological hypomenorrhea in the women from Southwestern China. Methods Totally 100 hypomenorrhea and 100 eumenorrhea women from Southwestern China served respectively as case group and control group. Restriction fragment length polymorphism (RFLP) was used to analyze the first intron incision enzyme PvuⅡ and XbaⅠin ER? gene. Short tandem repeat (STR) in hypervariable region of the gene was depurated, cloned and sequenced. The distribution of the gene genotype was studied in case group and control group. Results P genotypic frequency was 47.5% in case group, and 30.5% in control group (OR 1.810, 95%CI 1.113-2.765,P=0.012). While X genotypic frequency was 20.5% in case group and 32.0% in control group (OR 0.641, 95%CI 0.361-0.898, P=0.036). PvuⅡ and XbaⅠ restriction fragments were distributed in polymorphism in the 2 groups. The TA13 allele frequency was higher in case group than in control group (P