Heart failure (HF) is a complex clinical syndrome resulting from diverse primary and secondary causes, and shared pathways of disease progression, correlating with substantial mortality, morbidity and cost. HF in children is most commonly attributable to coexistent congenital heart disease (CHD), with different risks depending on the specific type of malformation. Current management and therapy for HF in children are extrapolated from treatment approaches in adults. This review discusses the causes, epidemiology and manifestations of HF in children with CHD, and presents the clinical, genetic and molecular characteristics that are similar or distinct from adult HF. The objective of this review is to provide a framework for understanding rapidly increasing genetic and molecular information in the challenging context of detailed phenotyping. We review clinical and translational research studies of HF in CHD including at the genome, transcriptome, and epigenetic levels. Unresolved issues and directions for future study are presented.