Medical geneticists must generate a differential diagnosis, practice evidence-based medicine, and apply ethical, legal, and social issue (ELSI) principles in the clinical setting. Several clinical scenarios are presented which illustrate dilemmas in the cancer genetics setting. These include the differential diagnosis of breast and gastric cancer, and the predicament posed by the need to practice evidence-based medicine in light of limitations in the medical genetics literature, which may mean recommending prophylactic surgery. Also discussed are three BRCA1/2 genetic testing scenarios which illustrate the difficulty of knowing where to “draw the line”, i.e., when to offer testing and what level of testing to pursue. Decision-making about BRCA1/2 gene testing including Ashkenazi Jewish founder mutation testing, comprehensive reflex testing, and expedited testing, is explored. The duty to recontact as standard of care evolves requires that medical geneticists determine how to prospectively set expectations with patients as well as to decide which situations require recontact and to determine how to systematically do so. The case of patient recontact regarding new mutation detection techniques with improved sensitivity, e.g., BART testing which is based on the ability to detect large BRCA1/2 rearrangements, is discussed. General principles are highlighted so that these specific cases can be extrapolated to other genes and hereditary conditions by medical geneticists, genetic counselors, and others practicing in the field of cancer genetics.