Background/aim: Bone disease is one of the most prominent complications after kidney transplantation. Bone diseases include osteoporosis, persistent secondary hyperparathyroidism, and avascular necrosis (AVN). We investigated the relationship between the polymorphisms of the vitamin D receptor (VDR) gene and bone diseases occurring after kidney transplantation. Materials and methods: The study consists of 234 kidney allograft recipients with a minimum follow-up of five years after kidney transplantation. Patients with glomerular filtration rates less than 30 ml/min/1.73m 2 , a history of parathyroidectomy, bisphosphonate use pre-or posttransplantation, and cinacalcet use post-transplantation excluded. We evaluated associations between the polymorphisms of the VDR gene (BsmI, TaqI, ApaI, FokI, and Cdx2), the first-year bone mineral density (BMD) scores, persistent secondary hyperparathyroidism, and AVN. Results: Patients with low BMD scores were significantly younger (p=0.03) and had higher intact parathormone (iPTH) levels (p=0.03). Cdx2 TT genotype significantly increases the risk of low BMD scores (OR:3.34, p=0.04). Higher phosphate levels were protective against abnormal BMD scores (OR:0.53; p=0.03). Patients with persistent hyperparathyroidism had significantly longer dialysis vintage and higher pretransplantation iPTH levels (p=0.02 and p<0.001, respectively). Cdx2, CT/TT, and ApaI CA/AA genotypes significantly increase the risk of persistent