Medical ethics is an indispensible and challenging aspect of clinical practice. This is particularly prominent in the field of organ transplantation. In this paper, initially, a clinical case with brain death that ended up as an organ donor will be presented. Following the presentation, important moral challenges which initially formed medical ethics and some highlights of it in organ transplantation will be discussed in detail. The impact of complex modern influential factors that might interfere with the practice of medical ethics in this field such as patients' vulnerability, financial temptations, and legal regulations will be also dealt with. Finally, we shall propose practical guidelines aiming at improving the practice of medical ethics in the emerging issue of organ transplantation.