We investigated the role of COL3A1 exon 31 polymorphism (a single base substitution from guanine to adenine at +2092), resulting in the replacement of alanine with threonine at the 698th amino acid of COL3A1, in the pathogenesis of pelvic organ prolapse. A total of 72 postmenopausal Korean women who were not on hormonal replacement therapy and who had a history of vaginal childbirth were enrolled in this study. The patient group consisted of 36 women diagnosed with stage II or greater pelvic organ prolapse irrespective of urodynamic stress incontinence. The control group consisted of 36 healthy volunteers with pelvic organ prolapse quantification system stage 0 or I disease without urodynamic stress incontinence. After extracting the genomic DNA from peripheral blood leukocytes the polymorphism of exon 31 of COL3A1 was typed by restriction fragment length polymorphism (Alu I restriction fragment length polymorphism) and confirmed by direct sequencing. Frequency of the G allele was significantly higher in patients with pelvic organ prolapse than in controls (0.8 vs 0.6, p = 0.002). In women with the G allele the OR for pelvic organ prolapse was 3.2 (95% CI 1.4-7.3). COL3A1 exon 31 polymorphism may have a role in determining the risk of pelvic organ prolapse in women with risk factors such as aging, vaginal childbirth and hypoestrogenism.