Congenital heart disease is the most common fetal abnormality resulting in high pediatric disability and mortality. Congenital heart disease is a heterogeneous group of cardiac abnormalities including atrial septal defect, valvular defects and cardiac outflow tract anomalies. Genetic, epigenetic and ecological factors leading to the development of congenital heart defects in each particular case remain poorly understood. Nevertheless, multifactorial and polygenic mechanisms underlying the disease may be suggested. Moreover, advanced genetic technologies including single nucleotide polymorphism testing, copy number variation and next-generation sequencing ensure early detection of genetic causes of heart abnormalities. Recent studies suggested the contributing role of small non-coding RNA (miRNA) in the pathogenesis of congenital heart defects. miRNA is known to coordinate the development of heart and stimulate such pathological processes like fibrosis, hypertrophy and impaired angiogenesis. Thus, the study of miRNA and its impact on the pathogenesis of various heart diseases has demonstrated its promising potential for therapeutic targets in regenerative medicine. The review presents recent genetic findings, miRNA functions, signaling pathways and evidences on its role in the development of certain congenital heart defects.