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Purpose: Although many studies have been performed to evaluate whether or not apolipoprotein E gene ( APOE) polymorphisms are differentially associated with bone mineral density (BMD) and fractures, the results have been conflicting. This large-scale study was performed to investigate whether a relationship exists between APOE polymorphisms and risk of fracture. Methods: A hospital-based case-control study was conducted in 3,000 patients with fractures and 3,000 age- and gender-matched healthy controls. Polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) assay was applied to assess the APOE gene polymorphisms. Results: Patients with fractures had a significantly higher frequency of APOE E2/E2 genotype [odds ratio (OR) = 2.02, 95 % confidence interval (CI) = 1.30, 3.14; P = 0.002] than healthy controls. When stratifying by fracture type, it was found that patients with vertebral fractures had a significantly higher frequency of APOE E2/E2 genotype (OR = 2.86, 95 % CI = 1.73, 4.73; P < 0.001). No significant differences were found in nonvertebral (hip or wrist or other) fractures. Conclusions: Our study suggests that APOE E2/E2 genotype is a potential genetic risk factor for vertebral fractures in humans. [ABSTRACT FROM AUTHOR]