Pelvic organ prolapse (POP) affects approximately 40% of elderly women, characterized by the descent of the pelvic organs into the vaginal cavity. Here we present the results of a genome-wide association study (GWAS) for susceptibility to POP comprising 771 cases and 76,625 controls in the Japanese population. We identified a significant association of
WT1
locus with POP in the Japanese population; rs10742277; odds ratio (OR) = 1.48, 95% confidence interval (CI), 1.29–1.68,
P
= 6.72 × 10
−
9
. Subsequent cross-ancestry GWAS meta-analysis combining the Japanese data and previously reported European data, including 28,857 cases and 622,916 controls, identified
FGFR2
locus as a novel susceptibility locus to POP (rs7072877; OR = 1.06, 95% CI, 1.04–1.08,
P
= 4.11 × 10
−
8
). We also observed consistent directions of the effects for 21 out of 24 European GWAS derived loci (binomial test
P
= 2.8 × 10
−
4
), indicating that most of susceptibility loci for POP are shared across the Japanese and European populations.