This article explores diverse ethical considerations related to the study of vulnerable population groups to produce meaningful project outcomes that avoid harm to the involved communities. In the specific context of the intersex community, previous analyses have encountered various challenges, including the medicalization of intersex people’s bodies, the use of pathologizing language, and misrepresentation of the population’s needs. The article explores some of the beliefs, experiences, and tools that experts in research ethics, researchers, and intersex research participants consider most important regarding research ethics in intersex-related studies. The article is based on original empirical research; semi-structured interviews were conducted with 21 participants, recruited through email and snowball sampling methods, and the data were examined using thematic analysis. It moves from issues related to the research design (positionality, researcher preparation, framing intersex within the LGBT acronym) to experiences related to the research development (ethical approval, informed consent process, language use, relationship of trust). The article describes some of the major concerns and raises discussions that could be relevant for the development of future research under human rights-based perspectives. The findings are aimed to be useful beyond the field of intersex-related studies, as they can be relevant to research about other communities that have endured violations of their human rights during research.