Use of information technologies in medicine resulted in formation of large databases. Analysis of large databases allows to reveal the patterns between the environmental conditions, a way of life and morbidity, that promote a progressive study of pathogenesis, clinical course, disease prognosis, and accelerate clinical trials of novel treatment options. Large databases are most in demand in bioinformatics and biomedicine. The issues of using large databases are associated with a number of ethical issues such as confidentiality, informed consent, and privacy. Ethical issues of using personal medical data were reflected in international documents. The use of large databases is associated with a dilemma of legislative protection of patients’ rights, on the one hand, and a decrease in analytical capabilities of using the data, on the other hand. Several methods of medical data safety are suggested to prevent identification of patients. Depersonilized data belong to one way of solving the issues. The options of studying secondary medical data are being discussed.