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Background: Data representing people’s behaviour, attitudes, feelings and relationships are increasingly being harvested from social media platforms and re-used for research purposes. This can be ethically problematic, even where such data exist in the public domain. We set out to explore how the academic community is addressing these challenges by analysing a national corpus of research ethics guidelines and published studies in one interdisciplinary research area. Methods: Ethics guidelines published by Research Councils UK (RCUK), its seven-member councils and guidelines cited within these were reviewed. Guidelines referring to social media were classified according to published typologies of social media research uses and ethical considerations for social media mining. Using health research as an exemplar, PubMed was searched to identify studies using social media data, which were assessed according to their coverage of ethical considerations and guidelines. Results: Of the 13 guidelines published or recommended by RCUK, only those from the Economic and Social Research Council, the British Psychological Society, the International Association of Internet Researchers and the National Institute for Health Research explicitly mentioned the use of social media. Regarding data re-use, all four mentioned privacy issues but varied with respect to other ethical considerations. The PubMed search revealed 156 health-related studies involving social media data, only 50 of which mentioned ethical concepts, in most cases simply stating that they had obtained ethical approval or that no consent was required. Of the nine studies originating from UK institutions, only two referred to RCUK ethics guidelines or guidelines cited within these. Conclusions: Our findings point to a deficit in ethical guidance for research involving data extracted from social media. Given the growth of studies using these new forms of data, there is a pressing need to raise awareness of their ethical challenges and provide actionable recommendations for ethical research practice.