The Prader-Willi syndrome and the Angelman syndrome are characterised by a complex clinical and behavioural phenotype resulting from loss of paternal or maternal expression, respectively, of genes located on the human chromosome 15q11-13. Different molecular mechanisms leading to this imbalance have been identified, including microdeletions, intragenic mutations, uniparental disomy and imprinting centre defects. Low copy repeat gene clusters are known to flank the 15q11-13 microdeletion. They predispose to unequal crossing-over events resulting in the deletion. Involvement of multiple disease genes is strongly suspected and traditional positional cloning techniques as well as animal models are used to identify the involved genes. In this review we include the present state of art and a delineation of future approach to study the candidate genes in these two syndromes.