BACKGROUND: Patient autonomy is a fundamental, yet challenging, principle of professional medical ethics. The idea that individual patients should have the freedom to make choices about their lives, including medical matters, has become increasingly prominent in current literature. However, this has not always been the case, especially in communist countries where paternalistic attitudes have been interwoven into all relationships including medical ones. Patients' expectations and the role of the doctor in the patient-physician relationship are changing. Croatia, as a transitional country, is currently undergoing this particular process. ----- METHODS: Qualitative research was conducted by means of six focus group discussions held in the years 2012 and 2013 in Croatia. Focus groups were held separately with each of the following: first year and final (6(th)) year medical students, physicians engaged in medical ethics education, physicians practicing in a clinical hospital, family medicine residents and individuals representing patients with chronic disease. This research specifically addresses issues related to patient autonomy, in particular, the principles of truth telling, confidentiality, and informed consent. All focus group discussions were audio taped and then transcribed verbatim and systematized according to acknowledged qualitative analysis methods. ----- RESULTS AND DISCUSSION: Patient autonomy is much more than a simple notion defined as the patient's right to make treatment decisions independently. It has to be understood in context of the broader socio-cultural setting. At present, both patients and medical doctors in Croatia are increasingly appreciating the importance of promoting the principle of autonomy in medical decision-making. However, the current views of medical students, physicians and patients reveal inconsistencies. ----- CONCLUSIONS: Knowing how to respect the various facets of patients' autonomy should be part of physician's professional duties, and also be reflected in his or her core clinical competencies. For this reason greater importance should be dedicated to patient autonomy issues in medical education in Croatia.