Whole genome sequencing (WGS) is increasingly being used in clinical practice. As a result, various healthcare professionals now encounter ethical dilemmas that were formerly confined within the genetics clinic. In addition to autonomy and well-being of both patients and their family members, which need to be balanced carefully, a societal perspective is also vital to ensure the ethically sound introduction of whole genome sequencing into daily practice. Important choices to be made are: who is eligible for whole genome sequencing; how can informed consent be sensibly obtained, when dealing with such vast quantities of genomic information; which type of information should be offered to patients; should professionals actively search for pathogenic mutations. The rise of WGS has an impact on the moral responsibilities incumbent on healthcare professionals and necessitates a comprehensive societal debate on the advent of personalized medicine.