The use of data in medical research that was originally collected for different purposes, known as secondary data, is an effective way to conduct reliable and cost-effective studies so as to progress knowledge in medicine. A number of serious practical, ethical and legal issues and concerns about this process exist, however. Ensuring a high level of data quality is imperative to produce reliable results, and researchers may face accessibility problems. Projects designed to alleviate these issues are underway, however, lowering the cost and increasing the access to secondary data even further. Although secondary data is de-identified to protect the confidentiality, ethical problems of individual rights versus the benefit of society persist, leading some to call for a new ‘macroethics’ surrounding data use. Legislation to this end has been introduced in many countries, but issues relating to the exemptions it offers and its interpretability remain. To ensure that the use of secondary data in medical research can continue to accelerate the pace of development in medicine, a global effort involving technological and ethical standardization needs to be developed.