Noncompaction/hypertrabeculation is increasingly being recognized in children and adults, yet we understand little about the causes of disease. Genes associated with noncompaction/hypertrabeculation have been identified, but how can these assist in clinical management? Genomic technologies have also expanded tremendously, making testing more comprehensive, but they also present new questions given the tremendous diversity of phenotypes and variability of genomes. Here we present genetic evaluation strategies and assess clinical testing options for noncompaction/hypertrabeculation. We assess genes/gene panels offered by clinical laboratories and the potential for high-throughput sequencing to fuel further discovery. We discuss challenges in cardiovascular genetics, such as interpretation of genomic variants, prediction and disease penetrance. © 2013 Wiley Periodicals, Inc.