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Background: Interest in children's agency within the research process has led to a renewed consideration of the relationships between researchers and children. Child protection concerns are sometimes not recognised by researchers, and sometimes ignored. Yet much research on children's lives, especially in health, has the potential to uncover child abuse. University research guidance should be in place to safeguard both researchers and the populations under scrutiny. The aim of this study was to examine university guidance on protecting children in research contexts. Methods: Child protection Standard Operating Procedures (SOPs) were requested from institutions with Research Assessment Exercise (2008) profiles in the top two quartiles according to published league tables. Procedures were included if they applied across the institution and if they were more extensive than stating the university's general application of the UK Disclosure and Barring Service process. A typology for scoring the SOPs was designed for this study based on the authors' previous work. The typology and the raw data scoring were reviewed independently by each of the team members and collectively agreed. The raw scores were charted and analysed using descriptive statistics. Results: SOPs for research conduct amongst vulnerable groups were sought from 83 institutions. Forty HEIs provided policies which met the inclusion criteria. The majority did not mention children, young people or vulnerable adults as a whole, although children in nurseries and young people in universities were addressed. Only three institutions scored over 50 out of a possible 100. The mean score was 17.4. More than half the HEIs made no reference to vetting/barring schemes in research, only eight universities set out a training programme on child protection. Research was often not mentioned in the SOPs and only six mention children in research, with only two fully recognising the extent of child protection in research. Discussion: There is potential for researchers to recognise and respond to maltreatment of children who participate in research. However, the majority of HEIs do not have an overt culture of safeguarding. There is confusion over what are the roles and responsibilities of HEIs in relation to research that involves children. Conclusions: The policies that are meant to support and guide research practice, so that children are protected, are in the most part non-existent or poorly developed. [ABSTRACT FROM AUTHOR]