Background The formation of the endocrinal cushion requires one of the members of the T-box transcription factor family, namely Tbx2. Yet, we have scarce information about the potential association of TBX2 3′ untranslated region (UTR) variations with congenital cardiac malformations. The aim of our study is the determination of the relationship between single-nucleotide polymorphism (SNP) rs59382073 in TBX2 3′ UTR and CHD susceptibility. Methods Venous blood samples were collected from 120 patients with CHD (encompassing 28 neonates, 72 infants, and 20 children) and additional 120 apparently healthy subjects and of matched age and sex. Genotyping of TBX2 3′UTR was performed using Step OnePlus PCR system using Taqman predesigned SNP assay (rs59382073). The distribution of genotype and allele frequency in both the congenital heart diseases (CHD) and the control groups were analysed. Results rs59382073 minor allele T carriers in TBX2 3′ UTR (homozygous TT and heterozygous GT subjects) had a significantly higher risk of CHD compared to wild-type GG subjects (OR 5.7; 95% CI, 2.99–11.1; P < 0.001 and OR 9.6; 95% CI, 3.1–29.6; P < 0.001), with the most likely subtypes being septal defect and conotruncal defects (P < 0.001 each). Conclusion T allele carriers of rs59382073 in TBX2 3′UTR had a greater risk of CHD than wild-type GG, septal defect and conotruncal defects were more common in T allele carriers than wild-type GG.