Objectives Collection and storage of biospecimens and data for biobanking raise many ethical concerns. Stakeholders' opinions about these ethical issues are important since they can help in the development of ethical guidelines to govern biobanking activities. Physicians are among the important stakeholders since they contact potential participants and could be biobank users. The goal of this study is to evaluate the perceptions and attitude of Egyptian physicians towards ethical issues in biobanking. Methods A cross-sectional online survey was designed and distributed with the target group between November 2019 and January 2020. Results The questionnaire was completed by 223 physicians. While 65.5% reported hearing the term "Biobanking" before, 45.7% knew that there are biobanks in Egypt. Participants had a general positive attitude towards the value of biobanks in research. About 73% agreed that biobanks can share biospecimens with international research organizations, but only 42.6% supported collaboration with pharmaceutical companies, and 44% agreed to the use of user fees by biobanks. About 48% supported the use of broad consent in biobanks, and 73.1% believed that donors of biospecimens should be informed about results of research performed on their biospecimens. Conclusion Although many Egyptian physicians heard about biobanking, they had limited knowledge about the existence of biobanks in Egypt. They had concerns about commercialization, use of broad consent and user fees. A knowledge gap exists among these stakeholders, which should be covered by different educational activities. Community discussions should start to reach consensus about the issues of commercialization and return of research results.