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This study reviews ethical issues encountered in the literature about the use of pharmacogenomics in personalized medicine. Data gathered from Medline, Scopus, and Scielo were grouped as issues belonging to the application of the four bioethical principles. Autonomy: informed consent with vulnerable populations, consent for biobanks, changes in the physician-patient relationship, safeguarding confidentiality; non-malifecence: risks of stigmatization and discrimination, risks in clinical trials; beneficence: risk/benefit assessment in favor of benefit; and justice: pharmacogenetic tests and public health interests, equity concerns. Issues discussed were: reasons in favor and against returning research results from genomic and pharmacogenetic testing, enhancing the participation of vulnerable populations, and the reconsideration of respect for autonomy from a viewpoint too individualistic to a communal perspective since personal reality is constructed in relation to many significant others.