Left ventricular outflow tract obstruction (LVOTO) is a wide spectrum of congenital heart defects ranging from bicuspid aortic valve to hypoplastic left heart syndrome. Increasing knowledge suggests a strong contribution of genetic factors in this disease spectrum. We have recruited a large cohort of multiplex families with LVOTO. All individuals gave informed consent and underwent physical exam, ECG and echocardiography. We have chosen 45 highly informative families and 23 trios for analysis of linkage and structural genomic variation using high-density genotyping (total cohort n = 450, affected = 217). To confidently call copy number variants, a phenotyped control cohort with 1900 members was used. In the 68 families analyzed to date, only one family with a clear Mendelian segregation pattern was identified. This family exhibits a novel X-linked syndrome with atrial septal defects, aortic valve disease, coarctation and atrial fibrillation. Significant linkage to Xq28 could be demonstrated, with a founder effect in a geographically confined area. In the cohort as a whole, significant linkage to chromosome 6q24 was found, defining an 8 Mb critical interval devoid of any obvious biological candidates and without any founder haplotypes. The analysis of copy number variants reveals 33 candidate loci in a highly complex pattern of inherited and de novo variants, 2/3 of which are gains. We provide a comprehensive high-density scan of LVOTO and identify linkage to two novel candidate loci in the French-Canadian population. Detailed haplotype analyses show conservation in a subset of families. Several layers of genetic factors most likely co-exist within this cohort, with structural genomic variation explaining the majority of phenotypic variability. These results pave the way towards a better definition of the causal genes and gene-gene interactions in LVOTO.