Though it has long been recognised that there is a hereditary component to the obstructive sleep apnoea/hypopnoea syndrome (OSAHS), identifying its genetic basis remains elusive. Hypertension and metabolic syndrome, like OSAHS, are polygenic disorders, physiologically complex and the product of highly organised, hierarchical systems within the body. Elucidating their genetic basis is difficult when they are considered in isolation but even more difficult if their interrelationships with each other are brought into play. Not least of the problems is the lack of adequate and consistent phenotyping, which has hampered genetic dissection of these diseases; in addition, sleep-disordered breathing has not been factored into most studies dealing with essential hypertension or metabolic syndrome. Genome-wide scans have yielded inconsistent results in all three disorders under discussion and candidate gene studies of possible regulatory molecules require more rigorous replication. One approach would be to use 'intermediate' phenotypes and dense mapping of candidate genes for identifying genotype-phenotype correlations. This review focuses on genetic factors, which may be responsible for the expression of cardiovascular disease and metabolic syndrome in the context of OSAHS.