The ability to detect polymorphic DNA sequence variants poses both opportunities for improved healthcare and concerns about the ethical challenges and confidentiality issues involved. Many polymorphisms confer only minor variability in disease susceptibility, which are difficult to detect and quantify, and therefore of minor value for improving healthcare. Important exceptions are high penetrance but uncommon disease susceptibility mutations, and those altering drug metabolism, knowledge of which should influence medical management. The development of Biobank initiatives to promote the detection and evaluation of important polymorphic variants highlights the need to ensure appropriate confidentiality guarantees and continuing debate about the ethical issues.