Pediatric cardiomyopathies are rare diseases, heterogeneous in clinical presentation, etiology and prognosis. Etiological diagnosis, where genetic analysis plays a key role, is of fundamental importance for defining diagnostic and therapeutic pathways. Furthermore, the identification of the genetic substrate represents a prerequisite for cascade screening in the proband's family members and to allow conscious reproductive choices. To date, genetic testing is performed with the analysis of gene panels (targeted panels) or with the study of the entire exome (whole exome sequencing) using next generation sequencing (NGS) technology. The great genetic heterogeneity and the temporal variability of the clinical manifestations lead to unique problems for pediatric cardiomyopathies, distinct from those of the adult, such as the possible indications for access to the test, the type of test to be used (exome or panel of genes), the importance of analyzing parents, especially in cases with neonatal onset; moreover, the correct execution of bioinformatics analysis and the interpretation of NGS data play a crucial role in the impact of the results on clinical management.