The diagnosis of osteoporosis is determined based on the lowest bone mineral density (BMD) T-score at the lumbar spine (LS) and hip. However, there are occasional marked discordances between the T-score of LS and femur neck (FN). We aimed to examine the prevalence and characteristics of individuals with spine-femur BMD discordance using a nationwide survey. A total of 3233 men aged ≥ 50 years and 2915 postmenopausal women were included from the Korean National Health and Nutrition Examination Surveys (2008-2011). The spine-femur discordance was defined as a difference of ≥ 1.5 SD between LS and FN BMD. Subjects were divided into three groups: low LS (LS < FN), low FN (LS > FN), and no discordance. Four-hundred and seventeen men (12.9%) and two hundred and ninety women (10%) exhibited spine-femur BMD discordance. The prevalence of hypertension and diabetes was higher in men and women with low FN BMD than in any other group. Fasting plasma glucose and homeostasis model assessment of insulin resistance was the highest in subjects with low FN BMD among the three groups. Low FN BMD revealed higher serum parathyroid hormone and lower 25-hydroxyvitamin D3 levels compared to any other group in women, but this was not observed in men. Osteoporosis was prevalent in subjects with discordance in both genders, particularly, in those with low LS BMD (31.6% in men and 63.5% in women). Given the high prevalence of spine-femur BMD discordance, low FN BMD may be associated with vitamin D deficiency and insulin resistance, but low LS BMD may present severe osteoporosis.