New discoveries using high-resolution methods for detecting genetic aberrations indicate that the genetic contribution to congenital heart disease has been significantly underestimated in the past. DNA diagnostics have become more accessible and genetic test results are increasingly being used to guide clinical management. Adult congenital heart disease specialists seeking to counsel adults with congenital heart disease about the genetic aspects of their condition face the challenge of keeping abreast of new genetic techniques and discoveries. The emphasis of this review is on the genetic basis of structural cardiovascular defects. A framework for identifying adult congenital heart disease patients most likely to benefit from genetic testing is suggested, along with a summary of current techniques for genetic testing. The clinical and ethical challenges associated with genetic counseling are highlighted. Finally, emerging technologies and future directions in genetics and adult congenital heart disease are discussed.