The course of normal heart formation in the embryo has been known for decades, but little is known about the genes that control its development. To further improve our understanding of the molecular and genetic mechanisms involved in congenital heart disease, we screened for submicroscopic chromosomal aberrations using bacterial artificial chromosome-based array comparative genomic hybridization analysis in two Danish twin pairs, one pair of monozygotic twins with tetralogy of Fallot, and one twin pair of unknown zygosity with pulmonary valve stenosis. We did not find any major chromosome defects, although a number of submicroscopic copy number variations were present. The question of whether these submicroscopic chromosomal imbalances alone or in conjunction with unknown intrauterine factors causes the observed cono-truncal malformations remains unanswered.