Background This is a multi-method, in-depth, three part qualitative study exploring the regulation and practice of secondary research with tissue and data in a high-income country. We explore and compare the perspectives of researchers, research ethics committees (RECs) and other relevant professionals (e.g. pathologists and clinicians). We focus on points of contention because they demonstrate misalignment between the expectations, values and assumptions of these stakeholders. Methods This is a multi-method study using observational research, focus groups and interviews with 42 participants (conducted 2016-2017) and analyzed using thematic analysis. Results Results are arranged under the following themes: consent; balancing the social value of the research with consent requirements; and harm. Our findings demonstrate different perspectives on the review process, styles of ethical reasoning and issues of concern. First, researchers and RECs disagreed about whether the cost of re-consenting patients satisfied the criterion of impracticability for consent waivers. Second, most researchers were skeptical that secondary research with already collected tissue and data could harm patients. Researchers often pointed to the harm arising from a failure to use existing material for research. RECs were concerned about the potential for secondary research to stigmatize communities. Third, researchers adopted a more consequentialist approach to decision-PLOS ONE