This study was performed to investigate the gene polymorphisms of the myeloperoxidase (MPO) enzyme and to determine whether MPO gene polymorphisms influence the response to iron therapy in pediatric patients with iron deficiency anemia (IDA). In this case-control study, 50 Turkish children with IDA and 50 healthy controls were enrolled. Three MPO gene alleles were selected for genotyping in the study: GG, AG, and AA. The relationships of alleles with IDA were analyzed and compared in patients and controls. Pretreatment and posttreatment laboratory parameters and gene polymorphisms were compared in the patient group. There was a significant difference between patients with IDA and controls regarding genotype frequencies of the AA, GG, and AG alleles (P=0.005). However, the AG allele was found to be associated with variations in hemoglobin, red blood cell, hematocrit, mean corpuscular volumes, and mean corpuscular Hb concentrations levels. The frequency of AA, GG, and AG alleles of the MPO gene was potentially associated with changes in iron metabolism and the AG allele led to variations in various hemogram parameters.