The aim of this study was to investigate the association of single-nucleotide polymorphisms (SNPs) and the DNA methylation profiles of the DNA methyltransferase (DNMT) gene family with oral mucositis in children and adolescents with hematologic malignancies treated with methotrexate (MTX®). The population was comprised of healthy and oncopediatric patients aged between 4 and 19 years. An evaluation of oral conditions was performed using the Oral Assessment Guide. Demographic, clinical, hematological, and biochemical data were obtained from medical records. Genomic DNA extracted from oral mucosal cells was used for the analysis of polymorphisms inDNMT1(rs2228611),DNMT3A(rs7590760), andDNMT3B(rs6087990) using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique (n= 102) and for DNA methylation using the methylation-specific PCR (MSP) technique (n= 85). The allele and genotypic frequencies of SNPs did not reveal any differences between patients with or without oral mucositis. An increase in the methylation frequency forDNMT1in patients recovered from mucositis was detected. TheDNMT3Amethylated profile associated with the CC genotype (SNP rs7590760) appeared to be connected to higher values of creatinine. In addition, theDNMT3Bunmethylated profile associated with the CC genotype (SNP rs6087990) appeared to be connected with higher values of creatinine. We conclude that theDNMT1methylation profile is associated with the post-mucositis period and that the genetic and epigenetic profiles ofDNMT3AandDNMT3Bare associated with creatinine levels.