Cow’s milk allergy (CMA) is one of the most frequent types of food allergy. The aim of the study was to investigate whether IL-13 R130Q and IL-4 T589C polymorphisms are associated with the risk of CMA in young Ukrainian children. A total of 120 children (age range: 1–3 years) participated in the study and were divided into two groups: CMA (n = 60) and healthy controls (CNT, n = 60). The CMA group had two subgroups: specific oral tolerance induction (SOTI, n = 30) and milk elimination diet (MED, n = 30). The CNT group had two subgroups: positive family history of allergy (+FHA, n = 24) and negative family history of allergy (−FHA, n = 36). In the CMA group, molecular genetic testing of CC, CT, and TT genotypes of single nucleotide IL-4 T589C gene polymorphisms showed significantly higher rates of the CC genotype compared to healthy controls (92.2% vs. 58.8%; p < 0.01). In the CMA group, molecular genetic testing of GG, GA, and AA genotypes of single nucleotide IL-13 R130Q gene polymorphisms showed significantly higher rates of GA and AA polymorphic locus genotypes compared to healthy controls (43.5% vs. 22.4%, p < 0.05 and 8.7% vs. 0%, p < 0.05, respectively). In future studies, the genotypic and allelic distribution of these polymorphic variants will be determined in children with CMA and healthy children.