Evaluation of bone mineralization and bone metabolism in children with inflammatory bowel disease (IBD) in accordance with TaqI-polymorphic genotypes of vitamin D receptor (VDR) has been performed in this study. 83 children (38 girls and 54 boys) with IBD (60 with Crohn’s disease, 23 with ulcerative colitis) have been included in the study. Mean age was 13.0 years (11.0; 15.5). All patients have active phase of the disease. Bone mineral density (BMD) of lumbar spine (DEXA) have been assessed in all children. Level of serum osteocalcin (OC) as a marker of osteosynthesis, C-terminal telopeptides (CTT) as a marker of osteoresorbtion, parathyroid hormone (PTH), serum calcium, phosphorus, alkaline phosphatase and 25(OH) vitamin D was measured to evaluate bone metabolism. Molecular-genetic tests: analysis of TaqI (rs731236) polymorphism of vitamin D receptor gene (VDR) was perfomed by polymerase chain reaction with following restriction analysis. Association between molecular markers of VDR gene and bone metabolism and mineralization disturbances have been found. TT genotype of VDR gene was associated with tendency to decrease of linear growth velocity, low linear growth, decrease in osteosynthesis and increase of osteoresorbtion in this group of children. TT-genotype of TaqI-polymorphism of VDR gene can be assessed as a risk factor of bone metabolism disturbances in children with both Crohn’s disease and ulcerative colitis. C allele seems to have protective role in this group.