Although obesity is known to have an influence on fracture, the relationship between lumbar and femur fractures and weight or waist circumference is controversial. We investigated the incidence of fracture with regards to waist circumference using the customised database of the Korean National Health Insurance Service (NHIS). Among 8,922,940 adults who participated at least twice in the NHIS National Health Check-up Program in South Korea between 2009 and 2011, 1,556,751 subjects (780,074 men and 776,677 women) were extracted. Over a mean follow-up of 6.5 years, multivariate-adjusted Cox regression analysis demonstrated that higher waist circumference was associated with an increased risk of femur fractures in both males and females. Moreover, the incidence of lumbar fracture was also positively associated with an increased waist circumference in males and females. An increased waist circumference showed a positive linear relationship with the risk of lumbar and femur fractures in both males and females.