Evidence on the association between abdominal obesity and vertebral fracture (VF) risk is limited. We examined the association of waist circumference (WC) and abdominal obesity with VF risk in 352,095 South Korean participants aged ≥40 years who underwent health checkups between 2009 and 2012. Abdominal obesity was defined by WC ≥90 cm in men and ≥ 85 cm in women according to the Asian-specific WC cutoff for abdominal obesity. Participants were a representative sample cohort of the Korean National Health Insurance System. The hazard ratios (HRs) and 95% CIs of VF development were determined using multivariable Cox proportional hazard regression analysis. During the 5.5 years of follow-up, there were 2030 and 4968 new cases of VF in men and women, respectively. In men, those with abdominal obesity showed an elevated HR (1.11, 95% CI:​ 1.01–1.23) of incident VF than did those without abdominal obesity. In women, the HRs of VF increased in higher WC groups after adjusting for confounders (P for trend <0.001);​ the HR decreased in those with WC <75.0 cm (HR:​ 0.81, 95% CI:​ 0.75–0.88) and increased in those with WC 85.0–89.9 cm (HR:​ 1.12, 95% CI:​ 1.02–1.22), 90.0–94.9 cm (HR:​ 1.19, 95% CI:​ 1.08–1.32), and ≥ 95.0 cm (HR:​ 1.27, 95% CI:​ 1.12–1.43) compared with those with WC 80.0–84.9 cm. This association persisted after stratification by age in women. WC and abdominal obesity were positively associated with VF risk in women, and abdominal obesity was associated with VF risk even in men. The consideration of WC and controlling abdominal obesity may be helpful in reducing future VF risk.